= 2007 - 2010 Chimera Change Log =

The following hand maintained list of changes was discontinued in Nov 2010,
replaced by a new [wiki:changelog change log] generated from our Trac ticket database.

{{{
#!html

<p>
This page lists changes to Chimera that are visible to users, including the
date and Chimera version when the change was checked in, and who made the
change (TG = Tom Goddard, AL = Andrew Ling).

<p><b>November 18, 2010</b></p>
<ul type=None>
<li><p>Fixed center of rotation command when only bond selected.
</ul>

<p><b>November 17, 2010</b></p>
<ul type=None>
<li><p>Added memory error check in benchmark scene drawing.
</ul>

<p><b>November 16, 2010</b></p>
<ul type=None>
<li><p>Added mean and standard deviation density calc for segmentation regions.
<li><p>Allowed fractional step in volume planes.
</ul>

<p><b>November 15, 2010</b></p>
<ul type=None>
<li><p>Fixed context help crash on mac, removed menu entry.
<li><p>Added warning for invalid cell angles in mrc file.
</ul>

<p><b>November 12, 2010</b></p>
<ul type=None>
<li><p>Added volume flattening divide method, applied to termite gut.
</ul>

<p><b>November 10, 2010</b></p>
<ul type=None>
<li><p>Improved attribute table and orthoslice viewing.
</ul>

<p><b>November 9, 2010</b></p>
<ul type=None>
<li><p>Worked around netcdf volume reading bug, ScientificPython.
</ul>

<p><b>November 5, 2010</b></p>
<ul type=None>
<li><p>Added segment sliceview command to make montage images.
<li><p>Added resize capability to segmentation image viewer.
<li><p>Fixed pick blobs error when everything is clipped.
<li><p>Fixed tiling order in orthoslice script, termite gut montages.
<li><p>Added fill order option to vop tile command.
</ul>

<p><b>November 3, 2010</b></p>
<ul type=None>
<li><p>Made measure contactarea ignore outline boxes.
</ul>

<p><b>November 2, 2010</b></p>
<ul type=None>
<li><p>Improved measure contact area patch smoothness.
<li><p>Added new color patterns for color by direction.
<li><p>Added vop tile operation to make section image montages.
</ul>

<p><b>November 1, 2010</b></p>
<ul type=None>
<li><p>Fixed error reporting to include callback info.
<li><p>Added segment directioncolor command.
</ul>

<p><b>October 29, 2010</b></p>
<ul type=None>
<li><p>Added measure distance command.
</ul>

<p><b>October 28, 2010</b></p>
<ul type=None>
<li><p>Fixed segmentation attribute table error for closed segmentation.
</ul>

<p><b>October 27, 2010</b></p>
<ul type=None>
<li><p>Implemented zone command.
</ul>

<p><b>October 26, 2010</b></p>
<ul type=None>
<li><p>Made segmentation attribute table remove unused columns.
</ul>

<p><b>October 22, 2010</b></p>
<ul type=None>
<li><p>Fixed morph map hang.
</ul>

<p><b>October 19, 2010</b></p>
<ul type=None>
<li><p>Debugged and fixed ScientificPython netcdf bindings code, 64-bit Windows.
</ul>

<p><b>October 11, 2010</b></p>
<ul type=None>
<li><p>Made mouse segmentation avoid showing all watershed regions.
</ul>

<p><b>October 6, 2010</b></p>
<ul type=None>
<li><p>Added measure command contact area operation.
<li><p>Made contact area account for partial triangles.
</ul>

<p><b>October 5, 2010</b></p>
<ul type=None>
<li><p>Improved error message when fetch from emdb fails.
<li><p>Fixed tube and ribbon shape ignoring specfied color with follow bonds.
</ul>

<p><b>October 4, 2010</b></p>
<ul type=None>
<li><p>Fixed shape tube followbonds option, ribbon band coloring.
<li><p>Fixed multiscale colors, made 64-bit same as 32-bit.
</ul>

<p><b>October 1, 2010</b></p>
<ul type=None>
<li><p>Added images to region attribute table and segmentation files.
<li><p>Added error handling when map size wrong when masking to region.
</ul>

<p><b>September 30, 2010</b></p>
<ul type=None>
<li><p>Added exporting region attributes as comma separated values.
<li><p>Implemented read and write of segmentation region attributes in hdf5.
<li><p>Simplified region attribute filter syntax, no more function calls.
</ul>

<p><b>September 29, 2010</b></p>
<ul type=None>
<li><p>Made measure spine region attributes appear in region list.
<li><p>Fixed sym command bug, two models for coord sys arg.
<li><p>Added filtering to region attribute list.
</ul>

<p><b>September 28, 2010</b></p>
<ul type=None>
<li><p>Made segmentation attribute browser using sortable table.
</ul>

<p><b>September 27, 2010</b></p>
<ul type=None>
<li><p>Checked in ribbon slice and curvature code.
</ul>

<p><b>September 24, 2010</b></p>
<ul type=None>
<li><p>Updated segger in chimera, segment unbin and show all fixes.
</ul>

<p><b>September 23, 2010</b></p>
<ul type=None>
<li><p>Fixed headless chimera movie recording.
</ul>

<p><b>September 22, 2010</b></p>
<ul type=None>
<li><p>Added curvature measurement to measure spine calculation.
<li><p>Implemented shape ribbon command to show bacteria center slices.
</ul>

<p><b>September 21, 2010</b></p>
<ul type=None>
<li><p>Added rectangle to shape command.
<li><p>Added connection failed error message, fit pdbs from emdb web service.
<li><p>Fixed byte order of machst in mrc files written by chimera.
<li><p>Made mac use immediate mode surf rendering for small surface pieces.
</ul>

<p><b>September 17, 2010</b></p>
<ul type=None>
<li><p>Fixed segment unbin so it shows region surfaces.
</ul>

<p><b>September 15, 2010</b></p>
<ul type=None>
<li><p>Fixed natural spline with single point, caused fly error.
<li><p>Fixed bug where mask ijk to xyz transform wrong when map closed.
<li><p>Fixed fit to segments closed mol, list reg number, transpar bugs.
</ul>

<p><b>September 14, 2010</b></p>
<ul type=None>
<li><p>Fixed fit to segments save fits menu entry.
</ul>

<p><b>September 13, 2010</b></p>
<ul type=None>
<li><p>Better error message when unable to write marker file.
<li><p>Fixed emdb fetch error causing hang.
<li><p>Fixed volume dialog session save with 2-d image stack.
<li><p>Fixed multiscale bug deleting chains.
<li><p>Fixed volume tracer bug opening marker set.
</ul>

<p><b>August 27, 2010</b></p>
<ul type=None>
<li><p>Allowed multiscale model creation without multiscale dialog existing,
allows nogui or headless Chimera use.
<li><p>Added surfaces keyword option to sym command for multiscale surfaces.
<li><p>Added biological unit button to model panel.
<li><p>Made multiscale use task manager when creating copies of molecules.
</ul>

<p><b>August 25, 2010</b></p>
<ul type=None>
<li><p>Fixed eman hdf file reading, python 2.7 / idle error.
</ul>

<p><b>August 6, 2010</b></p>
<ul type=None>
<li><p>Added list of fits to fit to segments dialog.
<li><p>Made volume dialog show value type in balloon when mouse over "Range"
dialog label (below histogram).
<li><p>Made gaussian filter use original data value type by default.  Formerly
it created a map with 32-bit float.
</ul>

<p><b>August 4, 2010</b></p>
<ul type=None>
<li><p>Fixed make transparent / opaque segment map menu entries when nothing selected.
</ul>

<p><b>August 3, 2010</b></p>
<ul type=None>
<li><p>Fixed fly command quaternion rotation interpolation.  Sometimes twirled
360 degrees for close orientations.
<li><p>Made fly command using natural cubic spline instead of Overhauser spline
for smoother paths.
<li><p>Made command file error halt processing and report error in reply log.
Formerly command processing continued even after an error in a script.
</ul>

<p><b>August 2, 2010</b></p>
<ul type=None>
<li><p>Fixed saving masked region with segment map dialog, bounds were wrong.
<li><p>Fixed render by attribute, numpy 1.4.1 int/long type problem.
<li><p>Fixed show adjacent error in segment map when some regions have no contacts.
<li><p>Fixed empty segmentation menu in segment map dialog.
<li><p>Fixed segment map hide menu entry not working on grouped regions.
<li><p>Fixed segger color density map error, numpy int/long problem.
</ul>

<p><b>July 27, 2010</b></p>
<ul type=None>
<li><p>Fixed watershed calc error 32-bit only, numpy 1.4 type error int/long.
</ul>

<p><b>July 22, 2010</b></p>
<ul type=None>
<li><p>Added movie crossfade command.
</ul>

<p><b>July 19, 2010</b></p>
<ul type=None>
<li><p>Fixed python 2.7 msms surface error on Windows.  Method for suppressing
console window for mscalc program no longer valid in python 2.7.
</ul>

<p><b>July 15, 2010</b></p>
<ul type=None>
<li><p>Made segment mouse mode accept clicks on single-plane volume.
<li><p>Fixed bug in solid coloring using mask, array size mismatch.
<li><p>Made group/ungroup buttons work when grouped subregions selected.
</ul>

<p><b>July 13, 2010</b></p>
<ul type=None>
<li><p>Implemented segment command unbin operation to apply a mask computed
on binned volume data to produce mask for the original full size volume data.
<li><p>Fixed coordset holdSteady option when jumping to a single frame.
</ul>

<p><b>July 9, 2010</b></p>
<ul type=None>
<li><p>Made segmentation not keep grid indices for each region.  This reduces
memory use of the segment map tool.
</ul>

<p><b>July 7, 2010</b></p>
<ul type=None>
<li><p>Added solid style volume coloring using a segmentation to the segment
map dialog (color density menu entry).  Formerly only colored volume surfaces.
</ul>

<p><b>July 6, 2010</b></p>
<ul type=None>
<li><p>Optimized measure spine command using small c++ routine, 59x faster.
</ul>

<p><b>July 2, 2010</b></p>
<ul type=None>
<li><p>Made spine diameter report orthogonal diameters at mid-point along
computed spine.
</ul>

<p><b>July 1, 2010</b></p>
<ul type=None>
<li><p>Made measure spine not need segmentation map open.
</ul>

<p><b>June 29, 2010</b></p>
<ul type=None>
<li><p>Fixed two bugs in fit to segments, neg corr, molmap replace
</ul>

<p><b>June 25, 2010</b></p>
<ul type=None>
<li><p>Improved imod seg file reader error message for non-IMOD files
<li><p>Made render-by-attribute dialog handle segmentation regions
</ul>

<p><b>June 23, 2010</b></p>
<ul type=None>
<li><p>Fixed solid volume memory leak, Solid.matrix held reference
<li><p>Made flatten filter use 64-bit float, needed for large maps
<li><p>Added measure spine command to compute bacteria paths and lengths
</ul>

<p><b>June 22, 2010</b></p>
<ul type=None>
<li><p>Made masking to regions handle full res maps with binned masks
</ul>

<p><b>June 21, 2010</b></p>
<ul type=None>
<li><p>Fixed dbpuppet ac_key_error messages, Laura Morris
<li><p>Implemented natural cubic spline, smoother than Overhauser spline
<li><p>Added vop unbend operation, straighten bacteria
<li><p>Wrote code to trace spine of bacteria automatically
</ul>

<p><b>June 17, 2010</b></p>
<ul type=None>
<li><p>Wrote code to unbend volume along path for straightening bacteria
</ul>

<p><b>June 1, 2010</b></p>
<ul type=None>
<li><p>Made segment mouse click on background show only ungrouped regions
</ul>

<p><b>June 14, 2010</b></p>
<ul type=None>
<li><p>Fixed cocoa open dialog nsscroller mouse click crashes
<li><p>Added segger to chimera distribution
</ul>

<p><b>June 10, 2010</b></p>
<ul type=None>
<li><p>Added "3d" shortcut to toggle between sequential stereo and mono
</ul>

<p><b>June 2, 2010</b></p>
<ul type=None>
<li><p>Fixed region delete bug in segment map
<li><p>Added flatten operation to volume filter dialog and vop command
<li><p>Improved mouse segmentation grouping to avoid start of drag abrupt group size change
</ul>

<p><b>June 1, 2010</b></p>
<ul type=None>
<li><p>Added gui for enabling segment grouping mouse mode
<li><p>Added ability to read old segger 1.4 regions files
</ul>

<p><b>May 28, 2010</b></p>
<ul type=None>
<li><p>Fixed mac universal build, tcltk docs not installed for debug version
<li><p>Added menu entries to show grouped and ungrouped segmentation surfaces
<li><p>Improved measure and color blobs to report sizes, boundary lengths
</ul>

<p><b>May 27, 2010</b></p>
<ul type=None>
<li><p>Allowed mouse mode grouping of single regions for blocking growth
<li><p>Made segment command to group regions using a second segmentation
<li><p>Fixed surface model front center, not ignoring hidden surface pieces
</ul>

<p><b>May 26, 2010</b></p>
<ul type=None>
<li><p>Made segmentation mouse mode detect clicked mask region, not density
<li><p>Made seg mouse mode show contacting regions after changing a region
<li><p>Added boundary region selection to find unclipped bacteria
</ul>

<p><b>May 21, 2010</b></p>
<ul type=None>
<li><p>Made mac ppc install debugging tcltk to avoid start-up crash
</ul>

<p><b>May 19, 2010</b></p>
<ul type=None>
<li><p>Made linux spacenavigator not print "connect error" to shell
<li><p>Made connectivity mouse mode make region groups that can be saved
</ul>

<p><b>May 13, 2010</b></p>
<ul type=None>
<li><p>Fixed tix combobox menu behind dialog on cocoa
<li><p>Fixed error deleting coord sys model during move command
</ul>

<p><b>May 12, 2010</b></p>
<ul type=None>
<li><p>Made debug graphics dialog not appear for new chimera version
<li><p>Separated segger into separate segmentation and fitting dialogs
</ul>

<p><b>May 11, 2010</b></p>
<ul type=None>
<li><p>Fixed cocoa inactive menus not gray, tk_setPalette cocoa tk bug
</ul>

<p><b>May 10, 2010</b></p>
<ul type=None>
<li><p>Made all chimera builds use tk 8.6
<li><p>Eliminated mac carbon builds
</ul>

<p><b>May 5, 2010</b></p>
<ul type=None>
<li><p>Made segger group and ungroup buttons change smoothing levels if nothing selected
<li><p>Allowed small region removal after segmenting
</ul>

<p><b>May 4, 2010</b></p>
<ul type=None>
<li><p>Added density map surface coloring by segmentation region
</ul>

<p><b>May 3, 2010</b></p>
<ul type=None>
<li><p>Worked around ctrl double click atom in graphics not showing menu, Eric
</ul>

<p><b>April 29, 2010</b></p>
<ul type=None>
<li><p>Fixed segger minimum region size option
<li><p>Made changing segger "max regions to display" have immediate effect
</ul>

<p><b>April 28, 2010</b></p>
<ul type=None>
<li><p>Optimized segger segmentation speed, about 5x speed-up
<li><p>Changed segger hdf5 file format for faster read and write, smaller file
</ul>

<p><b>April 27, 2010</b></p>
<ul type=None>
<li><p>Made watershed segmentation use 26 neighbors for local maxima instead of 6
<li><p>Added surface granularity parameter to segger
</ul>

<p><b>April 23, 2010</b></p>
<ul type=None>
<li><p>Preserved colors when using skeletons to edit a segmentation
</ul>

<p><b>April 21, 2010</b></p>
<ul type=None>
<li><p>Made segger read and write segmentation hdf5 file format
<li><p>Fixed eman hdf reader, pixel size
</ul>

<p><b>April 19, 2010</b></p>
<ul type=None>
<li><p>Eliminated intel and ppc processor-specific mac daily builds from download page
</ul>

<p><b>April 16, 2010</b></p>
<ul type=None>
<li><p>Sped up segger grouping by adding track to maximum routine to _segment module
<li><p>Avoided creating segger region surfaces unless needed.
</ul>

<p><b>April 15, 2010</b></p>
<ul type=None>
<li><p>Fixed linux space nav support, libspnav.so was not distributed
</ul>

<p><b>April 14, 2010</b></p>
<ul type=None>
<li><p>Made segger use new C++ module _segment for watershed calculation eliminating need for temporary file
</ul>

<p><b>April 13, 2010</b></p>
<ul type=None>
<li><p>Made transform coordinates dialog work with non-molecules
<li><p>Added skeleton routines and menu to segger
</ul>

<p><b>April 6, 2010</b></p>
<ul type=None>
<li><p>Fixed bug in volume filter casting int16 -> uint16 bug where all values became 65535
<li><p>Fixed wrong normals when contouring unsigned data
<li><p>Made segger filtering small regions use connected size
</ul>

<p><b>March 29, 2010</b></p>
<ul type=None>
<li><p>Fixed fetch directory preference not saving, was requiring Enter key press
</ul>

<p><b>March 25, 2010</b></p>
<ul type=None>
<li><p>Fixed bug where center-of-view rotation not updating
</ul>

<p><b>March 17, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Fixed front-center to not move center during rotation.
<li><p>Made opening pdb on command-line look for compressed local files.
<li><p>Made opening python scripts not clear globals when finished.
<li><p>Made turn keyword center accept "view", "models", "front".
<li><p>Disabled silhouette outline drawing for volumetric rendering.
</ul>

<p><b>March 16, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Worked around cocoa bug unicode arrow keys in entry fields.
<li><p>Fixed saxs profile calc to work with more than one molecule.
</ul>

<p><b>March 15, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Made saxs gui give better error if local execution fails.
</ul>

<p><b>March 9, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Put max number of regions to display in segger dialog.
<li><p>Fixed segger bug, grouped regions remain displayed.
</ul>

<p><b>March 8, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Fixed arrow key menu shortcuts / cursor motion bug, cocoa.
</ul>

<p><b>March 5, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Made segger not accumulate smoothing when done twice.
</ul>

<p><b>March 3, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Remade segger dialog, added progress/cancel, menu reset, options pane...
<li><p>Made segger save of region and map files show a file chooser dialog.
</ul>

<p><b>March 2, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Fixed missing cocoa menu check-marks, tk patch.
<li><p>Made pdb personal directories try hierarchical layout.
</ul>

<p><b>March 1, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Added tk cocoa patch to fix option-e crash.
</ul>

<p><b>February 23, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Made default movie recording use variable bit rate, q = 8.
<li><p>Debugged and fixed new ffmpeg bit rate in bits/sec instead of Kbits/sec.
</ul>

<p><b>February 21, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Worked around cocoa user interface lock-out on cocoa.
</ul>

<p><b>February 19, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Made close command accept multiple models.
<li><p>Fixed reset command to work with now unhashable xform objects.
</ul>

<p><b>February 18, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Made write command allow "#" preceding model number.
</ul>

<p><b>February 17, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Made segger calculate sim map automatically for groups of regions.
<li><p>Made measure inertia report center of ellipsoid.
</ul>

<p><b>February 8, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Changed segger to show pastel region colors.
<li><p>Fixed segger axes alignment and normal direction.
</ul>

<p><b>February 5, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Included 32-bit / 64-bit info in benchmark submissions.
<li><p>Made chimera About dialog report 32-bit or 64-bit.
</ul>

<p><b>February 4, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Added ppc mac cocoa and cocoa universal daily build targets.
</ul>

<p><b>February 3, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Fixed tk cocoa open/save double click by having no default button.
<li><p>Made 17 small user interface improvments to segger.
</ul>

<p><b>February 1, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Added error checking in movie record command option values.
</ul>

<p><b>January 29, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Started 64-bit mac daily builds using Tk Cocoa and NSOPENGL.
</ul>

<p><b>January 22, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Made gaussian cube file reader handle skewed data axes.
</ul>

<p><b>January 20, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Fixed movie recorder dialog bug, director not initialized.
</ul>

<p><b>January 19, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Debugged cocoa actions/color menu not showing, images freed while in use.
<li><p>Fixed cocoa application menu and wrong dock icon.
</ul>

<p><b>January 15, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Debugged cocoa model panel wrapped text, patched tix.
</ul>

<p><b>January 13, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Added color images to cocoa chimera color menu.
<li><p>Fixed model panel scroll down-only, reported aqua tk bug, 2931538.
<li><p>Allowed raytrace and supersample movie record options to change.
</ul>

<p><b>January 12, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>SAX dialog fixes, raise dialog, remember empty executable pref.
</ul>

<p><b>January 11, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Started making cocoa daily builds with Tk 8.6.
</ul>

<p><b>January 6, 2010. Version 1.5</b></p>
<ul type=None>
<li><p>Added progress/cancel to gaussian filter using new task manager.
</ul>

<p><b>January 5, 2010. Version 1.4.1</b></p>
<ul type=None>
<li><p>Made side view cap clipped surfaces button only show dialog.
<li><p>Made model panel focus button enable near/far clipping.
</ul>

<p><b>December 21, 2009. Version 1.5</b></p>
<ul type=None>
<li><p>Optimized gaussian filter to use efficient fft sizes.
<li><p>Made gaussian filter not-cyclic wrap, 2x speed penalty.
<li><p>Made gaussian filter more memory efficient, compute one plane at a time.
</ul>

<p><b>December 15, 2009. Version 1.4.1</b></p>
<ul type=None>
<li><p>Fixed movie recorder dialog size parsing error.
</ul>

<p><b>December 9, 2009. Version 1.5</b></p>
<ul type=None>
<li><p>Fixed keyboard shortcuts dialog to list all shortcuts.
<li><p>Added filter entry to keyboard shortcut dialog.
</ul>

<p><b>December 8, 2009. Version 1.5</b></p>
<ul type=None>
<li><p>Made volume session not precede relative paths with './' or '.\'.
</ul>

<p><b>December 4, 2009. Version 1.5</b></p>
<ul type=None>
<li><p>Made shape command default coordinate system use surface model.
</ul>

<p><b>December 3, 2009. Version 1.5</b></p>
<ul type=None>
<li><p>Added rotation, qrotation, name arguments to shape command.
<li><p>Added ellipsoid to shape command.
</ul>

<p><b>November 25, 2009. Version 1.5</b></p>
<ul type=None>
<li><p>Removed phantom force feedback tool from distribution.
</ul>

<p><b>November 24, 2009. Version 1.5</b></p>
<ul type=None>
<li><p>Made top view mode of side view dialog always show focal plane.
<li><p>Fixed focal plane behind eye black-out bug.
<li><p>Added movement mouse mode to structure editing menu.
</ul>

<p><b>November 23, 2009. Version 1.4</b></p>
<ul type=None>
<li><p>Made dialog auto-placement not override session restore placement.
<li><p>Made session restore not place dialogs off-screen.
</ul>

<p><b>November 20, 2009. Version 1.4</b></p>
<ul type=None>
<li><p>Fixed aqua menu response by delaying menu post by 1 msec.
</ul>

<p><b>November 17, 2009. Version 1.4</b></p>
<ul type=None>
<li><p>Fixed front-center rotation updating too often.
<li><p>Fixed morph map on volume subregion.
</ul>

<p><b>November 8, 2009. Version 1.4 and 1.5</b></p>
<ul type=None>
<li><p>Added use new plot window option to saxs dialog, default false (Chimera 1.5).
<li><p>Added mw molecular weight shortcut (Chimera 1.4).
</ul>

<p><b>November 6, 2009. Version 1.4</b></p>
<ul type=None>
<li><p>Fixed uninitialized memory errors, no init of surfnet grid.
</ul>

<p><b>November 3, 2009. Version 1.4</b></p>
<ul type=None>
<li><p>Added Linux space navigator support.
</ul>

<p><b>November 2, 2009. Version 1.4</b></p>
<ul type=None>
<li><p>Fixed morph map error when volume closed during playback
</ul>

<p><b>October 30, 2009. Version 1.5</b></p>
<ul type=None>
<li><p>Added fit in map correlation about zero option, the default.
<li><p>Made meshmol command produce model with new id number.
</ul>

<p><b>October 28, 2009. Version 1.5</b></p>
<ul type=None>
<li><p>Added msms warning message for wrong number of atom areas.
<li><p>Optimized memory use in resampling maps.
</ul>

<p><b>October 16, 2009. Version 1.4</b></p>
<ul type=None>
<li><p>Made fit map gray out optimize and whole molecule options when not avail.
</ul>

<p><b>October 15, 2009. Version 1.4</b></p>
<ul type=None>
<li><p>Removed SAXS module.
<li><p>Removed volume processing standalone programs from distribution.
</ul>

</p>
<p><b>October 8, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made match command showMatrix argument print motion from current position
in addition to motion from original file coordinates.
<li><p>Don't print rotation when fitting only selected atoms with
Fit in Map dialog.
</ul>

<p><b>October 7, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added fit dialog option to optimize correlation about zero instead of correlation about mean.
<li><p>Made fit dialog option to move only selected atoms instead of whole
molecules.
<li><p>Added undo/redo motion buttons to fit dialog.
</ul>

<p><b>October 6, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made session merge not savepos session-start if that position already
exists.
<li><p>Replaced matrixcopy relativeTo keyword with "moving" keyword.
<li><p>Made set light_quality command update quality in lighting dialog.
<li><p>Added check for matching grid sizes in vop morph command.
<li><p>Made vop cover update rendering options of source map -- was setting
those options but failed to show them.
<li><p>Fixed session merging error handling of old sessions.
</ul>

<p><b>October 2, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added hide command-line to bottom of command history menu.
<li><p>Made session merge keep old window size and camera/viewer settings.
</ul>

<p><b>October 1, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made vrml models not use glossy shader, avoids black vrml objects.
</ul>

<p><b>September 30, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed glossy lighting fog so alpha is not used.  Needed so that
100% transparent surfaces are invisible.
<li><p>Added showSlabs option to measure rotation command.
<li><p>Improved file fetch error on socket errors which are not IOError.
<li><p>Added relativeXform option to matrixcopy to fix misaligned sessions.
<li><p>Made session merging align old and new lowest id models.
</ul>

<p><b>September 29, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added update keyword to sym command, default false.
<li><p>Added toggle outline box shortcut "ob".
</ul>

<p><b>September 28, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made selection object model order follow vertex order.  Allows
vop add command to get correct model order.
<li><p>Fixed surface zone session restore bug with molecular surfaces.
<li><p>Added minRMS option to vop subtract for subtracting fit maps.
<li><p>Made vop subtract operation use interpolation like vop add.
</ul>

<p><b>September 25, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made vop add not extend grid due to round-off if grids are identical.
<li><p>Added multipliers arg to vop add.
<li><p>Made open viper:1bbt fetch from viperdb instead of pdb.
</ul>

<p><b>September 18, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made ~surf command close molecular surfaces with closed molecules.
</ul>

<p><b>September 17, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed fit in map, with simulated map didn't move atoms.
<li><p>Made measure buriedarea report buried areas for both atom sets.
</ul>

<p><b>September 16, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made mz shortcut place marker at origin in selected models local coords.
<li><p>Added center and axis arguments to sym command.
</ul>

<p><b>September 15, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added symmetry group argument to sym command.
</ul>

<p><b>September 14, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Improved color zone out-of-memory error message.
</ul>

<p><b>September 11, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added move molecule mouse mode.
</ul>

<p><b>September 10, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Implemented vop cover operation for periodic map extension.
</ul>

<p><b>September 9, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed vanishing surface cap on Windows.
</ul>

<p><b>September 7, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed pseudobondgroup bounding box calculation, wrong coordinate system.
<li><p>Added playDirection, playRange and addMode options to vop morph command.
<li><p>Fixed front-center, was using mid-depth even when model intercepted.
<li><p>Fixed color parsing error in measure inertia.
</ul>

<p><b>September 4, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added vop morph command.
<li><p>Added number of cells option to unit cell dialog.
<li><p>Made unit cell outline button toggle outline off.
</ul>

<p><b>September 3, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added options panel to unit cell dialog.
</ul>

<p><b>September 2, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made unit cell dialog handle inverting symmetries.
</ul>

<p><b>August 31, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made marker note labels set using actions label menu save in sessions.
<li><p>Fixed bug where deleting marker did not delete residue.
<li><p>Fixed split map by color bug, numpy array in sessions.
</ul>

<p><b>August 25, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added command "set light_quality glossy|normal".
</ul>

<p><b>August 24, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made surface color dialog show offset field only for electrostatics.
</ul>

<p><b>August 21, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Translated mesh subdivision python to c++ for faster calculation.
<li><p>Made error dialog not report full traceback, just a few lines.
<li><p>Fixed shape command color parsing, was generating an error.
<li><p>Made surface zone and color zone save arrays as strings in session files.
<li><p>Fixed shape command, was adding to existing surface when none specified.
</ul>

<p><b>August 20, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Saved surface data as strings in sessions, smaller files and faster
save and restore.
</ul>

<p><b>August 19, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed aqua double menu posting bug.
<li><p>Fixed shape command model id parsing error.
<li><p>Added sop surface operation command. The finerMesh operation
subdivides surface meshes to have uniform edge length.
<li>Added offset keyword to scolor command to allow coloring by volume data
or volume gradient at a position offset from a surface along the surface
normals.  The offset can be a single signed float value, or a range given by
two values start, end, and an integer N (e.g. offset 0,8.5,4) specifying that
N offsets should be used and the average volume value used.  This is for
coloring by projecting a slab of volume data.
<li><p>Made mouse rotation center allow z and xy rotation when model
rotation center is far off screen.  The xy-rotation region of the window now
always includes a circle centered on the window with diameter half the window
size (minimum of window width and height).
</ul>

<p><b>August 18, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed error when overwriting missing volume data file.
<li><p>Fixed bug where volume selection outline box used new molecule
preferences.
</ul>

<p><b>August 17, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added linux space navigator support contributed by Thomas Margraf.
</ul>

<p><b>August 14, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made volume data contour calculation catch memory allocation exception
so Chimera does not crash.
</ul>

<p><b>August 12, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made molmap command allow specifying map subid.
</ul>

<p><b>August 11, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Updated saxs profile calculation user interface, no longer requires
form factor file.
</ul>

<p><b>August 10, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made initial molecule display style not apply to volume tracer
marker models.
</ul>

<p><b>August 7, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed volume eraser error caused by new volume tracer api.
<li><p>Added surface color dialog offset option for electrostatic coloring.
<li><p>Fixed tile command argument parsing error.
</ul>

<p><b>August 5, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added tube display to shape command.
</ul>

<p><b>August 4, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made volume tracer tubes use surface model instead of vrml.
</ul>

<p><b>August 3, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed volume outline box to avoid coloring and capping.
<li><p>Made volume flip normals for thresholds less than 0 default off.
<li><p>Added tile command.
<li><p>Made volume save command handle multifile save with %d index.
</ul>

<p><b>July 31, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed subsampled grid data caching, caused blank histogram display.
<li><p>Added vop boxes operation to extract subregions around markers.
</ul>

<p><b>July 29, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made volume tracer work without graphical user interface.
<li><p>Added vop median and scale filter operations.
</ul>

<p><b>July 28, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Replaced vop and volume command use_step/use_subregion arguments with step/subregion.
<li><p>Fixed imod reader bug, error reading point size records.
</ul>

<p><b>July 24, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added measure inertia command for molecules and surfaces.
</ul>

<p><b>July 22, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made scale filter clamp integer values to data type limits.
<li><p>Changed frame update timers to assure minimum event processing time.  Prevents some lock-outs during continuous rendering on aqua.
<li><p>Fixed broken mask command.
<li><p>Made mask command ignore hidden parts of surface.
</ul>

<p><b>July 21, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made molmap accept a # character in the modelId argument.
</ul>

<p><b>July 20, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed binning filter step size bug.
</ul>

<p><b>July 17, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Changed vop syntax, operation first arg, rejects invalid keywords.
<li><p>Fixed meshmol bug, error due to obsolete volume tracer call.
</ul>

<p><b>July 16, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made session saving eliminate indent on long lists, smaller file size.
<li><p>Fixed emdb fetch bug where xml and web service used when not needed.
</ul>

<p><b>July 15, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed bug in vop permute, permutation incorrect.
</ul>

<p><b>July 14, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added vop add command.
<li><p>Added useGridStep, useGridSubregion, boundingGrid vop resample options.
<li><p>Made volumes with unicode filenames open.
</ul>

<p><b>July 13, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added set/reset and cumulative transform to molecule transform dialog.
<li><p>Updated to pytables 2.1.1 to allow reading Chimera map format files with unicode file names.
</ul>

<p><b>July 10, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made fit in map only use displayed subregion when counting points outside contour.
</ul>

<p><b>June 23, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed non-orthogonal rotation errors in reading profec volume maps.
<li><p>Fixed gross memory inefficiency writing map file.  Was reading a full copy of map for every plane for formats that could not read submaps.
<li><p>Made mouse rotation virtual sphere center be the model center of rotation.
</ul>

<p><b>June 22, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed incorrect default center for scolor command.
</ul>

<p><b>June 19, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed per-pixel surface color bugs with transparent surfaces.
<li><p>Implemented scolor command for surface color dialog functionality.
</ul>

<p><b>June 18, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed surface transparency color hierarchy problems.
</ul>

<p><b>June 17, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added frames argument to surftransparency command.
<li><p>Made surftransparency command work on non-msms surfaces.
</ul>

<p><b>June 12, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Fixed session save error with empty marker set.
</ul>

<p><b>June 10, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added bin operation to vop command.
</ul>

<p><b>June 9, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Implemented volume binning filter.
<li><p>Made per-pixel surface color use colormap end values instead of black.
<li><p>Fixed per-pixel surface color lighting.
</ul>

<p><b>June 5, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made pick blobs and volume tracer work with per-model clipped surfaces.
</ul>

<p><b>June 4, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added volume tracer mouse mode for marker placement on surfaces.
<li><p>Put each volume tracer marker in its own residue to allow specifying
numeric ranges in commands.
</ul>

<p><b>June 3, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added mask command invertMask option.
<li><p>Added caps argument to shape command for cylinder caps.
</ul>

<p><b>June 2, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made copy/paste work in aqua for bug report dialog "gathered info" field.
<li><p>Fixed morph map movie record bug, backslash t in file interpreted as tab.
</ul>

<p><b>May 29, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Added per pixel coloring to surface color dialog using textures.
<li><p>Made surface textures support luminance and border colors.
<li><p>Updated function names for emdb web service search.
</ul>

<p><b>May 27, 2009.  Version 1.4</b></p>
<ul type=None>
<li><p>Made transparent texture coloring of surfaces work.
<li><p>Added texture coloring to surface color dialog.
<li><p>Fixed bug where 3d texture not updated when color mode changed.
<li><p>Fixed bug where volume color mode not updated when switching between 2d and 3d solid style.
</ul>


<p><b>May 20, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed space navigator lag and poor response on aqua. TG
<li><p>Fixed actions missing some models with no selection when multiscale surfaces present. TG
</ul>

<p><b>May 19, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made emdb web search show citation and map release date. TG
<li><p>Made fetch panel show search field only for searchable databases. TG
</ul>

<p><b>May 18, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made volume save command handle "~" paths. TG
</ul>

<p><b>May 11, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made reply dialog text selectable and copyable on aqua. TG
<li><p>Made ~/Desktop/xxx paths work on windows. TG
</ul>

<p><b>May 7, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made movie encoding friendly error if output directory doesn't exist. TG
</ul>

<p><b>May 1, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added tilde expansion to movie encoding output path. TG
</ul>

<p><b>April 30, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed demo auto-play sometimes freezing Chimera.  Aqua Tk menu callback bug. TG
</ul>

<p><b>April 27, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added silhouette, depth cue, subdivision "set" command options. TG
<li><p>Added coordset command to play trajectories, for movie scripts. TG
</ul>

<p><b>April 24, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made command-` and shift-command-` cycle aqua windows. TG
<li><p>Removed aqua focus follows mouse code and preference setting. TG
<li><p>Made emdb fetch use web service to find fit pdbs, was using xml file. TG
</ul>

<p><b>April 20, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made multiscale copy isHet to avoid water chaining. TG
</ul>

<p><b>April 15, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made mac aqua tk use click-through. TG
</ul>

<p><b>April 9, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed fetch dialog to hide when return key pressed in id field. TG
</ul>

<p><b>April 7, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed export obj bug where wrong material file path written. TG
</ul>

<p><b>March 30, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added memory error check in volume filter. TG
</ul>

<p><b>March 25, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added emdb search capability to fetch by id dialog. TG
</ul>

<p><b>March 24, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed bug where last used data matrix for a volume not kept in cache. TG
<li><p>Increased volume data default cache size to 512 Mb, was 32 Mb. TG
</ul>

<p><b>March 20, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added slab option to shape command. TG
<li><p>Made mcopy copy bond properties, fixed label copy. TG
</ul>

<p><b>March 19, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed mcopy bug, coordinate copy did not work. TG
</ul>

<p><b>March 16, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed bug in dock grid error message. TG
<li><p>Made clip command give user-friendly near>far error message. TG
</ul>

<p><b>March 13, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made modbase and castp fetch use downlaod directory. TG
</ul>

<p><b>March 12, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made pubchem fetch use download directory. TG
</ul>

<p><b>March 11, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed fly command bug where an extra frame count was used. TG
<li><p>Made color command handle r,g,b,a numeric color arguments. TG
<li><p>Added fetching emdb maps to fetch-by-id dialog. TG
<li><p>Added button to fetch by id dialog shows download directory preferences. TG
<li><p>Added cancel link in progress messages to cancel fetch operation. TG
<li>Enabled uncompressing fetched data files. TG
<li>Made bondcolor and colordef handle r,g,b,a numeric arguments. TG
</ul>

<p><b>March 10, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added mcopy command to copy molecule settings. TG
<li><p>Added fetch-by-id download directory for eds, viperdb, pqs, pdb, cif, scop, ndb. TG
</ul>

<p><b>March 6, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made all command color arguments accept tk colors, comma-separated rgba. TG
</ul>

<p><b>March 5, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made volume scale filter respond when enter key pressed. TG
</ul>

<p><b>March 4, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made measure rotation mention coordinate system in reply log output. TG
<li><p>Made measure and vop keyword abbreviations work and case insensitive. TG
<li><p>Made rotation axis color be model color. TG
<li><p>Allowed markers/links to have no color, uses molecule color. TG
<li><p>Improved per-model clipping shorcuts cc, ca and removed tc. TG
<li><p>Made scale/shift volume filter update when filter settings changed. TG
</ul>

<p><b>February 26, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed saving markers as xml when atoms/bonds deleted. TG
</ul>

<p><b>February 25, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added showAxis option to measure rotation command. TG
</ul>

<p><b>February 20, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed molmap to work with molecules with different transforms. TG
<li><p>Made stl export for 3-d printing. TG
</ul>

<p><b>February 17, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made matrixcopy handle multiple destination models. TG
<li><p>Made shape command hide some mesh edges for icosahedron and cylinder. TG
<li><p>Added lighting attributes, normals, edge mask to surface session save. TG
<li><p>Made color zone with bond zone respect half-bond coloring. TG
</ul>

<p><b>February 13, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added silhouette edge drawing for transparent models. TG
<li><p>Added one layer and all layers transparency menu entries. TG
<li><p>Fixed multiscale bug where chain associated with original molecule
deleted, and other surfaces recalculated at new resolution. TG
<li><p>Fixed bug where volume session restore tried to set solid model
orientation when that model did not exist. TG
<li><p>Fixed bug where opening solid model did not set initial camera view. TG
</ul>

<p><b>February 11, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made session save include molecular surface attributes: smoothing,
lighting on/off, two-sided lighting, dot and line widths. TG
<li><p>Added one transparent layer surface option.  Added equivalent option
to volume dialog surface and mesh panel. TG
<li><p>Added shortcuts t5 and t0 to make surfaces 50% and 0% transparent. TG
</ul>


<p><b>February 10, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made move/turn/rock/roll move inactive models when "models"
keyword used. TG
<li><p>Made open volumes use absolute paths even if specified with relative
paths so that data can be read later if current working directory changed. TG
</ul>

<p><b>February 9, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Improved rendering of multiple transparent surface models so model
behind does not appear in front. TG
</ul>

<p><b>January 28, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made multiscale contacts not select chain surfaces when atoms of
chain are selected. TG
</ul>

<p><b>January 21, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Wrote fly command to smoothly interpolate positions/camera. TG
</ul>
<p><b>January 20, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed swapped buried ses/sas area atom attributes. TG
</ul>

<p><b>January 19, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed reset with frame count error when model closed. TG
<li><p>Made volume surface outline box unlit when using glossy lighting. TG
<li><p>Fixed bug where hide dust turned volume square mesh into triangles. TG
</ul>

<p><b>January 18, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Made hdf map read use planes along smallest chunk shape axis. TG
<li><p>Added use step/subregion/zone options to volume save command. TG
<li><p>Added scale/shift/cast operation to volume filter dialog. TG
<li><p>Added permuteaxes operation to vop command. TG
</ul>

<p><b>January 16, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed bug in histogram calculation that caused slightly incorrect
volume threshold. TG
y<li><p>Added buried area to measure command. TG
</ul>

<p><b>January 15, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed matplotlib on windows, wasn't finding tcl/tk headers. TG
<li><p>Fixed turn/roll/rock bug, inactive models moved when center specified. TG
</ul>

<p><b>January 14, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed shader code to not throw error on compile/link info messages. TG
<li><p>Fixed esp coloring bug, coloring method not set. TG
<li><p>Fixed bright edges from glossy lighting, had diffuse light on
both sides of surface. TG
<li><p>Made correlation matplotlib plot use tk instead of native Mac window. TG
</ul>

<p><b>January 13, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed bug move,turn,roll,rock coordinateSystem arg not working. TG
<li><p>Fixed disappearing light arrows in light panel. TG
<li><p>Made turn/roll/rock/move use coord system of center or axis spec. TG
</ul>

<p><b>January 9, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added matplotlib 2d plotting library to distribution, used for showing
correlation of map with rotated map. TG
</ul>

<p><b>January 8, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added correlation for rotated map positions to measure command. TG

</ul>

<p><b>January 7, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Wrote measure command to show rotation axis connecting two models. TG
<li><p>Handle new delphi map format on mac with 64 bit floats. TG
<li><p>Made turn,roll,rock,move accept 2 atom or bond spec for axis. TG
<li><p>Added surface volume and area to measure command. TG
<li><p>Added map correlation to measure command. TG
<li><p>Made glossy lighting not apply to unlit lines, caused dim molecule
wires. TG
y</ul>

<p><b>January 6, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Added median filtering to filter dialog. TG
<li><p>Added clip volume (cv), clip adjust (ca), glossy lighting (gl)
shortcuts. TG
<li><p>Made clip and cap shortcut act on selected model, not show dialogs. TG
<li><p>Fixed bug where single color volume solid dimmed by factor
of red component. TG
</ul>

<p><b>January 2, 2009.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed bug where surface cap not updated when mask changed. TG
<li><p>Added options panel to gaussian filter dialog, including
immediate update option. TG
<li><p>Made filter dialog adjust thresholds for constant volume
use the enclosed volume for the gaussian filtered volume rather than
the original volume. TG
<li><p>Made Filter button just update existing volume
if active volume is a gaussian filtered volume. TG
</ul>

<p><b>December 30, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Moved per-pixel lighting option from effects panel to lighting panel. TG
<li><p>Fixed mac x11 start error when glossy lighting preference not supported. TG
<li><p>Fixed bug where glossy mode sometimes had no effect because
graphics context was not current when setting shader. TG
</ul>

<p><b>December 29, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Allowed depth cue start >= 1 for back lighting effect. TG
<li><p>Made surface cap use only visible parts of surfaces, helps castp. TG
</ul>

<p><b>December 19, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Added "glossy" lighting mode using an opengl shader providing
per-pixel lighting and angle-dependent transparency. TG
</ul>

<p><b>December 18, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Replace depth cue yon intensity parameter with end depth. TG
</ul>

<p><b>December 16, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Added slider to control width of gaussian filter. TG
</ul>

<p><b>December 10, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Added hide dust tool that hides small connected surface blobs. TG
<li><p>Increased surface cap default offset 0.001 to 0.01 to avoid disappearing
caps. TG
<li><p>Made sum of gaussians routine (used by molmap) able to take
different standard deviations along 3 axes for PALM/STORM microscopy data. TG
</ul>

<p><b>December 9, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Disabled used of Chimera user interface while volume data load is loaded,
allowing only cancel of data load. TG
<li><p>Moved volume auto display subregion option from data display panel to
subregion selection panel. TG
<li><p>Allowed volume auto-cropping (resampling) with rotated subregion box.
With solid style rendering this does a good job of showing slices that are not
parallel to the volume box faces. TG
</ul>

<p><b>December 8, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Fixed subregion resampling box when source map has local rotation. TG
<li><p>Debugged blank volume histogram when session restored,
cache size not set before volume dialog created. TG
</ul>

<p><b>December 5, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Added session saving for icosahedron tool. TG
</ul>

<p><b>December 3, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Provide user-friendly error message when molecular surface calculation
produces truncated output. TG
<li><p>Suppress Mac 10.5 crash report dialog when molecular surface calculation
fails. TG
</ul>

<p><b>November 25, 2008.  Version 1.4</b></p>

<ul type=None>
<li><p>Made move selection mouse mode able to move surface pieces. TG
</ul>

<p><b>November 21, 2008.  Version 1.2577.</b></p>

<ul type=None>
<li><p>Made initial volume viewer thresholds symmetric about 0 for 
electrostatic potential data and other polar data. TG
<li><p>Added gaussian and laplacian filters to vop command. TG
</ul>

<p><b>November 20, 2008.  Version 1.2576.</b></p>

<ul type=None>
<li><p>Made per-model clipping work with solid volume rendering where
projection mode is perpendicular to view (uses 3d textures).
</ul>

<p><b>November 19, 2008.  Version 1.2576.</b></p>

<ul type=None>
<li><p>Fixed error reading mrc file > 2 Gbytes. TG
</ul>

<p><b>November 18, 2008.  Version 1.2575.</b></p>

<ul type=None>
<li><p>Fixed hkcage command error when invoked second time with surface
capping enabled. TG
<li><p>Added planes keyword to volume command to show sequence of planes. TG
<li><p>Made turn, move, ... not raise error if model deleted during motion. TG
<li><p>Added volume outline box linewidth setting. TG
<li><p>Fixed reset command to preserve relative orientations. TG
</ul>

<p><b>November 17, 2008.  Version 1.2575.</b></p>

<ul type=None>
<li><p>Fixed bug that caused extra frames during movie capture scripts
that read volume data, caused by progress messages. TG
<li><p>Made movie encode command print status messages on main status line. TG
</ul>

<p><b>November 14, 2008.  Version 1.2575.</b></p>

<ul type=None>
<li><p>Fixed incorrect center of rotation when a model is closed where another
model has the same id. TG
<li><p>Made actions / focus with nothing selected turn of near/far clipping. TG
</ul>

<p><b>November 13, 2008.  Version 1.2574.</b></p>

<ul type=None>
<li><p>Suppress Mac 10.5 crash report dialog when molecular surface 
calculation mscalc program crashes. TG
<li><p>Fixed volume command bug setting color of solid rendering. TG
</ul>

<p><b>November 12, 2008.  Version 1.2574.</b></p>

<ul type=None>
<li><p>Fixed bugs writing image stacks as single hdf (*.cmap) files. TG
</ul>

<p><b>November 11, 2008.  Version 1.2574.</b></p>

<ul type=None>
<li><p>Made molecule bounds include atom radii to avoid clipping atom spheres
when near/far clipping is turned off. TG

<li><p>Fixed error closing volumes when new session opened. TG
<li><p>Fixed bug where distant opaque solid volume models appeared in front of
closer opaque soild volume models. TG
<li><p>Fixed bug where restored traced surface not saved in subsequent sessions.
TG
</ul>

<p><b>November 10, 2008.  Version 1.2574.</b></p>

<ul type=None>
<li><p>Added warning when restoring a session file written by a newer chimera
version. TG
<li><p>Fixed bug restoring volume / surface coloring from session files written
by Chimera version more than 1 year old. TG
</ul>

<p><b>November 6, 2008.  Version 1.2573.</b></p>

<ul type=None>

<li><p>Fixed volume eraser bug introduce Sept 30. TG
</ul>

<p><b>November 4, 2008.  Version 1.2573.</b></p>

<ul type=None>
<li><p>Made surface capping on by default. TG
<li><p>Made space navigator preserve front-center rotation point during
rotation. TG
</ul>

<p><b>November 3, 2008.  Version 1.2573.</b></p>

<ul type=None>
<li><p>Made near/far clip planes off by default. TG
</ul>

<p><b>October 31, 2008.  Version 1.2572.</b></p>

<ul type=None>
<li><p>Made surface bounds calculation use bounding sphere instead of box
resulting in tighter bounds for sphere-like surfaces. Effects amount of camera
zoom when the first model show is a surface. TG
</ul>

<p><b>October 29, 2008.  Version 1.2572.</b></p>

<ul type=None>
<li><p>Changed default surface transparency blend model to dim (alpha,1-alpha).
TG
<li><p>Added center of rotation mode name options "fixed", "front", "models",
and "independent" to cofr command. TG
<li><p>Made coordinateSystem arguments to movement commands work without '#'. TG
</ul>

<p><b>October 28, 2008.  Version 1.2571.</b></p>

<ul type=None>
<li><p>Fixed failure to hide clicked triangle using pick blobs tool. TG
<li><p>Cleared surface visibility/color atom attributes when surface closed. TG
</ul>

<p><b>October 27, 2008.  Version 1.2571.</b></p>

<ul type=None>
<li><p>Fixed bug where hiding a molecular surface piece made subsequent surface
show not work. TG
</ul>

<p><b>October 24, 2008.  Version 1.2571.</b></p>

<ul type=None>
<li><p>Changed the default center of rotation mode to front-center. TG
<li><p>Fixed multiscale session save error that happened after chain deleted. TG
</ul>

<p><b>October 22, 2008.  Version 1.2569.</b></p>

<ul type=None>
<li><p>Added front-center center of rotation mode. TG
<li><p>Added coordinate system, center, models arguments to turn, roll, rock,
	 and move commands. TG
<li><p>Made benchmark dialog show warning if models are open. TG
<li><p>Allowed move command to move along all 3 axes at once. TG
<li><p>Made cofr command accept point coordinates and coord sys arguments. TG
<li><p>Added center, coord system, model id args to shape command. TG
</ul>

<p><b>October 20, 2008.  Version 1.2567.</b></p>

<ul type=None>
<li><p>Made options panel for morph map and added roundtrip option. TG
</ul>

<p><b>October 15, 2008.  Version 1.2566.</b></p>

<ul type=None>
<li><p>Fixed actions menu entries focus, set pivot, surface
hide/show/repr/tranparency and color when a molecular surface is selected
but not its atoms. TG
</ul>

<p><b>October 14, 2008.  Version 1.2566.</b></p>

<ul type=None>
<li><p>Made focus command and action use center-of-models when nothing selected.
TG
<li><p>Fixed session saving error after closing traced surface model. TG
</ul>

<p><b>October 10, 2008.  Version 1.2566.</b></p>

<ul type=None>
<li><p>Fixed model panel configure dialog bug, pmw tabs not raising in
Mac Aqua Chimera. TG
</ul>

<p><b>October 1, 2008.  Version 1.2561.</b></p>

<ul type=None>

<li><p>Made molecular surface show "all components" false in selection
inspector if all-component calculation failed and instead used single-component.
TG
<li><p>Fixed volume show/hide icon update error on model close. TG
</ul>

<p><b>September 29, 2008.  Version 1.2561.</b></p>

<ul type=None>
<li><p>Added memory checking to c++ python array allocation used in volume
and surface calculations. TG
</ul>

<p><b>September 25, 2008.  Version 1.2561.</b></p>

<ul type=None>
<li><p>Added ls keyboard shortcut to open last session file. TG
</ul>

<p><b>September 23, 2008.  Version 1.2560.</b></p>

<ul type=None>
<li><p>Fixed volume solid color mode and projection mode bugs. TG
</ul>

<p><b>September 19, 2008.  Version 1.2559.</b></p>

<ul type=None>
<li><p>Added out-of-memory test for large surfaces. TG
<li><p>Turn off mesh lighting for single plane volume display. TG
<li><p>Made volume planes switch to solid style only when "one" button pressed.
TG
<li><p>Made single plane volume contour surface without capping render with
mesh to show 2d contours. TG
</ul>

<p><b>September 12, 2008.  Version 1.2558.</b></p>

<ul type=None>
<li><p>Added fourier transform to vop command, removed fourier transform
menu entry. TG
</ul>

<p><b>September 11, 2008.  Version 1.2558.</b></p>

<ul type=None>
<li><p>Made volume square mesh option show box cap diagonals.
The square mesh code that excluded box cap diagonals also excluded all
contours for single data planes. TG
<li><p>Added volume planes cycle option with plane count and speed control.
Replaces "play" button. TG
<li><p>Added button to volume planes panel to preload data. Allows faster
moving through planes. TG
</ul>

<p><b>September 10, 2008.  Version 1.2558.</b></p>

<ul type=None>
<li><p>Fixed volume tracer bug where first marker on empty space mispositioned
if no models are opened. TG
</ul>

<p><b>September 9, 2008.  Version 1.2558.</b></p>

<ul type=None>
<li><p>Changed volume dialog origin field to show index of xyz origin instead
of xyz coordinates of index 0,0,0. Allows changing voxel size without altering
xyz origin position within array. TG
<li><p>Added originIndex keyword to volume command for specifying the xyz origin
in grid index units.  Changing voxelSize with volume command now preserves
index of xyz 0,0,0 rather than xyz of index 0,0,0. TG
<li><p>Added single volume plane surface and mesh display.  Allows drawing
2d contour lines.  Formerly surface and mesh style volume display showed
nothing for single planes. TG
</ul>

<p><b>September 8, 2008.  Version 1.2557.</b></p>

<ul type=None>
<li><p>Made solid volume rendering status messages about color appear
only once per frame. Were showing for every data plane. TG
<li><p>Fixed erratic incorrect use of x or y projection axes in solid
rendering. TG
<li><p>Fixed netcdf out of memory error message. TG
<li><p>Fixed bugs where volume dialog did not update display style and
hide/show icon when solid style hidden (and hence solid model closed). TG
</ul>

<p><b>September 5, 2008.  Version 1.2557.</b></p>

<ul type=None>
<li><p>Added luminance color for volume rendering so single color modes need
not display white. TG
<li><p>Added auto projection mode that chooses 2d z planes rendering volume
slabs with aspect 4:1 or greater, otherwise xyz planes (using more memory). TG
</ul>

<p><b>September 3, 2008.  Version 1.2554.</b></p>

<ul type=None>
<li><p>Removed colormap mode from solid style volume rendering. TG
</ul>

<p><b>September 2, 2008.  Version 1.2554.</b></p>

<ul type=None>
<li><p>Changed electrostatic surface coloring to be opaque red/white/blue. TG
</ul>

<p><b>August 29, 2008.  Version 1.2554.</b></p>

<ul type=None>
<li><p>Added volume projection mode option for tomogram viewing using solid
style.  Allows only showing z planes.  3x less memory use versus xyz mode
where planes most parallel to screen used. More memory efficient. TG

<li><p>Change volume solid style rendering to not make full 3-d temporary color
array. Instead computes only 2-d color planes at a time.  Reduces memory use. TG
</ul>

<p><b>August 28, 2008.  Version 1.2554.</b></p>

<ul type=None>
<li><p>Added support for volume color pixel formats (opengl texture
format): RGB, luminance/alpha, luminance, 4,8,12 or 16-bit.  Formerly
only RGBA 8-bit used.  More memory efficient, faster transfer to
graphics card, allows display of larger maps.
</ul>

<p><b>August 27, 2008.  Version 1.2554.</b></p>

<ul type=None>
<li><p>Fixed color zone session restore bug on msms surfaces. TG
</ul>

<p><b>August 26, 2008.  Version 1.2553.</b></p>

<ul type=None>
<li><p>Updated surface model programmer's guide documentation. TG
<li><p>Made morph map not report error on reset/cancel movie recording. TG
</ul>

<p><b>August 25, 2008.  Version 1.2552.</b></p>

<ul type=None>
<li><p>Sped up volume plane display solid rendering 2x by reusing color array. TG
</ul>

<p><b>August 22, 2008.  Version 1.2552.</b></p>

<ul type=None>
<li><p>Delayed volume dialog histogram and range updates to speed up
cycling through volume planes. TG
<li>Optimized speed of volume plane display. TG
</ul>

<p><b>August 21, 2008.  Version 1.2552.</b></p>

<ul type=None>
<li><p>Added Chimera video documentation to web site. AL
<li><p>Changed implementation of solid style volume rendering with
colormaps to not use opengl pixel transfer. Avoids graphics driver
bug on GeForce 7300 Mac graphics. TG
<li><p>Made solid volume colormap use 8-bit color values instead of float,
more memory efficient. TG
</ul>

<p><b>August 20, 2008.  Version 1.2552.</b></p>

<ul type=None>
<li><p>Made imod file reader to correctly handle open vs closed contours. TG
<li><p>Added support uint8 rgba color values in solid rendering, more
memory efficient. TG
</ul>

<p><b>August 19, 2008.  Version 1.2552.</b></p>

<ul type=None>
<li><p>Removed broken spotlight help/search menu entry on aqua mac 10.5. TG
<li><p>Fixed color_by_volume() routine used in scripts. TG
</ul>

<p><b>August 15, 2008.  Version 1.2550.</b></p>

<ul type=None>
<li><p>Added 8-bit color indices for solid volume rendering, more
memory efficient.  Formerly only 16-bit indices used. TG
</ul>

<p><b>August 14, 2008.  Version 1.2550.</b></p>

<ul type=None>
<li><p>Made surface color tool ignore volume outline boxes. TG
</ul>

<p><b>August 13, 2008.  Version 1.2550.</b></p>

<ul type=None>
<li><p>Making imod file reader properly skip unused records. TG
<li><p>Updated tomoplane extension to new surface model api. TG

</ul>

<p><b>August 12, 2008.  Version 1.2549.</b></p>

<ul type=None>
<li><p>Fixed bug where closing volume series removed wrong entry from menu. TG
</ul>

<p><b>August 1, 2008.  Version 1.2549.</b></p>

<ul type=None>
<li><p>Fixed black covering status line on aqua when graphics window
resized smaller. TG
</ul>

<p><b>July 31, 2008.  Version 1.2548.</b></p>

<ul type=None>
<li><p>Added focus follows mouse preference, only shown and used on aqua. TG
</ul>

<p><b>July 30, 2008.  Version 1.2547.</b></p>

<ul type=None>
<li><p>Fixed pif map bug where integer file values scaled by floating point
scale factor remained as an integer map.  Caused sparse histograms. TG
<li><p>Made volume cap facing initially off for PIF maps since they are
most often inverted. TG
<li><p>Made marker resize mouse mode use caps lock instead of alt key. TG
<li><p>Added option to hide in-window menus on aqua. TG
</ul>


<p><b>July 29, 2008.  Version 1.2546.</b></p>

<ul type=None>
<li><p>Moved create color key button to options panel. TG
</ul>


<p><b>July 28, 2008.  Version 1.2546.</b></p>

<ul type=None>
<li><p>Put new movie making tutorial on chimera tutorials and
animations web pages. TG
</ul>

<p><b>July 23, 2008.  Version 1.2544.</b></p>

<ul type=None>

<li><p>Made volume series update histograms for all series.  Was only updating
one when multiple series played simultaneosly. TG
<li><p>
</ul>

<p><b>July 22, 2008.  Version 1.2544.</b></p>

<ul type=None>
<li><p>Made volume series tool handle multiwavelength priism data. TG
<li><p>Made volume series tool allow playing all series at once. TG
<li><p>Fixed memory leak when volumes created and closed. Data array
was deallocated but not surface model and volume python object. TG
<li><p>Added showDialog option to molmap command to suppress display of
volume dialog (useful in MD trajectory per-frame scripts). TG
<li><p>Made fetch eds able to set model id on command-line. TG
</ul>

<p><b>July 21, 2008.  Version 1.2544.</b></p>

<ul type=None>
<li><p>Fixed bug when volume data read canceled on opening,
session save failed. TG
</ul>

<p><b>July 18, 2008.  Version 1.2544.</b></p>

<ul type=None>
<li><p>Made volume series tool copy changes in voxel size and volume origin. TG
<li><p>Fixed bug saving volume over original file on a different file system
than /tmp (file move didn't work). TG
<li><p>Fixed bug where msms calculation says it succeeded but actually returns
an incorrect empty surface. TG
<li><p>Fixed movie recorder ffmpeg encoding on aqua, trouble reporting status
from non-gui thread.  Disabled status reporting on aqua. TG
<li><p>Made movie recorder not raise main window when doing image capture. TG
</ul>

<p><b>July 15, 2008.  Version 1.2542.</b></p>

<ul type=None>
<li><p>Fixed bug, surface color wrong if volume moved while data is being
read. TG
<li><p>Fixed space navigator lag on aqua. TG
</ul>

<p><b>July 9, 2008.  Version 1.2540.</b></p>

<ul type=None>
<li><p>Production release Chimera 1.2540.
</ul>

<p><b>July 8, 2008.  Version 1.2540.</b></p>

<ul type=None>

<li><p>Fixed bug where NaN volume normals caused raytracing failure. TG
</ul>

<p><b>July 7, 2008.  Version 1.2540.</b></p>

<ul type=None>
<li><p>Made vop resample command undisplay original instead of
grid volume. TG
<li><p>Fixed volume dialog shown/hidden indicator updating for new volumes. TG
<li><p>Made crash report dialog on mac not appear for 
mscalc crashes (msms surface calculation). TG
</ul>

<p><b>July 2, 2008.  Version 1.2540.</b></p>

<ul type=None>
<li><p>Fixed aqua bug: patched pmw to make open dialog history popup menus
appear on top. TG

</ul>

<p><b>July 1, 2008.  Version 1.2537.</b></p>

<ul type=None>
<li><p>Made volume solid style coloring properly color min/max data values. In
some cases the data values corresponding to the end nodes on the volume
histogram were not colored. TG
<li><p>Fixed molecule copies behavior of crystal contacts tool
and added command version. TG
</ul>

<p><b>June 30, 2008.  Version 1.2537.</b></p>

<ul type=None>
<li><p>Optimized morph map, 8x faster linear combination on 256^3 array. TG
<li><p>Made vop resample command use better name for new volume. TG
<li><p>Fixed aqua bug: patched pmw notebook bubble buttons and borders for
aqua tk 8.5.2. TG

</ul>

<p><b>June 27, 2008.  Version 1.2537.</b></p>

<ul type=None>
<li><p>Fixed aqua bug: clipped volume plane button text and feature buttons. TG
<li><p>Fixed volume show/hide icon in volume dialog in solid mode. Sometimes
showed incorrect display state. TG
</ul>

<p><b>June 26, 2008.  Version 1.2537.</b></p>

<ul type=None>
<li><p>Added mS shortcut to place markers on selected atoms. TG
</ul>

<p><b>June 25, 2008.  Version 1.2537.</b></p>

<ul type=None>
<li><p>Added aqua in-window menubars for all dialogs: castp,
selection workbench, modbase, rotamers, render by attr, viewdock, demo, movie,
multalign. TG
</ul>

<p><b>June 24, 2008.  Version 1.2535.</b></p>

<ul type=None>
<li><p>Fixed aqua bug: disappearing bonds (stick style) and vrml cylinders
when zooming. TG
<li><p>Fixed aqua bug: playing morph map gave volume dialog focus
prevented stopping morph playback. TG
<li><p>Fixed aqua bug: mouse scroll wheel zooming very insensitive. TG
</ul>

<p><b>June 19, 2008.  Version 1.2534.</b></p>

<ul type=None>
<li><p>Fixed volume dialog surface brightness and transparency sliders.
They were producing color component values > 1 causing error messages. TG
<li><p>Made command-q and the main window close button show the quit
confirmation dialog on aqua. TG
</ul>

<p><b>June 18, 2008.  Version 1.2532.</b></p>

<ul type=None>
<li><p>Added in-window menu bars to volume and tracer dialog windows in aqua. TG
<li><p>Added vop subtract operation for making difference maps. TG
<li><p>Fixed volume histogram flickering on aqua. TG
</ul>

<p><b>June 17, 2008.  Version 1.2531.</b></p>

<ul type=None>
<li><p>Fixed divide by zero warning message appearing in shell when
using volume solid style rendering with opacity = 1. TG
</ul>

<p><b>June 16, 2008.  Version 1.2531.</b></p>

<ul type=None>
<li><p>Fixed error when deleting volumes caused by trying to update
volume shown indicator (dash icon) after deletion. TG
<li><p>Added option/command key 3-button mouse emulation in aqua. TG
</ul>

<p><b>June 13, 2008.  Version 1.2531.</b></p>

<ul type=None>

<li><p>Added MacMolPlt/Gamess quantum orbitals volume file reader. TG
</ul>

<p><b>June 12, 2008.  Version 1.2531.</b></p>

<ul type=None>
<li><p>Made volume viewer and volume tracer show menu bar at top of screen
on aqua. TG
</ul>

<p><b>June 11, 2008.  Version 1.2529.</b></p>

<ul type=None>
<li><p>Fixed display of headings in preferences tools pane on aqua. TG
<li><p>Added focus follow mouse mode for aqua. TG
</ul>

<p><b>June 10, 2008.  Version 1.2527.</b></p>

<ul type=None>
<li><p>Made opening electrostatic potential file formats (delphi, apbs, uhbd)
and molecular orbital file formats (gaussian, gopenmol) turn of box face
surface capping so that negative threshold levels do not result in box surface.
TG
<li><p>Fixed actions menu surface transparency on molecular surfaces colored
by molecule. TG
<li><p>Made in-memory writable volumes created by volume eraser have names
ending in "copy" to distinguish them from original volumes. TG
<li><p>Made opening volume file not use data from already opened writable
volume since that data may be modified later. TG
<li>Fixed aqua 60% cpu usage when showing model panel, but in tix
scrolledhlist with headers. TG
</ul>

<p><b>June 9, 2008.  Version 1.2527.</b></p>

<ul type=None>
<li><p>Made model menus use multiple columns on x11 if they have more than
35 entries to avoid inaccessible entries off bottom of screen. TG

<li><p>Made saving volume data update the volume name in volume dialog
and menus. TG
</ul>

<p><b>June 6, 2008.  Version 1.2525.</b></p>

<ul type=None>
<li><p>Made surface display use opengl vertex buffer objects instead of display
lists, leading to 2x faster rendering on two tested graphics cards. TG
</ul>

<p><b>June 5, 2008.  Version 1.2525.</b></p>

<ul type=None>
<li><p>Made priism volume file reader set correct voxel size. TG
<li><p>Made molecular surface display for a set of atoms not override
partial surface display done with surface zone tool. TG
<li><p>Made active volume name highlighting on aqua use blue color. Was using
white which was identical to inactive background. TG

<li><p>Made main window have focus at startup on aqua. TG
</ul>

<p><b>June 3, 2008.  Version 1.2525.</b></p>

<ul type=None>
<li><p>Fixed hang on aqua caused by benchmark dialog horizontal scrollbar
display/undisplay. TG
<li><p>Fixed aqua bug where movie recorder could not be stopped because
graphics window was given focus at each frame preventing pressing the Stop
button. TG
<li><p>Fixed aqua bug where movie recorder could not find ffmpeg executable. TG
</ul>

<p><b>June 2, 2008.  Version 1.2525.</b></p>

<ul type=None>
<li><p>Made priism volume file reader handle xywzt and xyzwt data orders
(w = wavelength, t = time). TG

</ul>

<p><b>May 30, 2008.  Version 1.2524.</b></p>

<ul type=None>
<li><p>Fixed molecular surface bug where closing surface model and then
reshowing surface for subset of atoms showed entire surface. TG
<li><p>Made toolbar and model panel balloons not take focus in aqua. TG
</ul>

<p><b>May 28, 2008.  Version 1.2523.</b></p>

<ul type=None>
<li><p>Padded selection button in lower right corner of main window so that
text is not clipped on aqua. TG
<li><p>Made atom spec balloons on aqua not have window frame, and not take
focus. TG
<li><p>Added apple application menu entries for About Chimera... and
Preferences... on aqua. TG

<li><p>Made model panel Select button work on molecular surfaces. TG
</ul>

<p><b>May 27, 2008.  Version 1.2522.</b></p>

<ul type=None>
<li><p>Fixed volume image stack session saving bug. TG
<li><p>Fixed recently introduced bug where color byatom with a surface shown
generated an error. TG
<li><p>Fixed aqua chimera crash when any dialog shown by disabling apple event
handling code. TG
</ul>

<p><b>May 26, 2008.  Version 1.2522.</b></p>

<ul type=None>
<li><p>Made actions atom/ribbon/surface menus work with multiscale models. TG

</ul>

<p><b>May 22, 2008.  Version 1.2517.</b></p>

<ul type=None>
<li><p>Made space navigator work with independent center of rotation mode. TG
<li><p>Made select command on surfaces select all the surface pieces. TG
</ul>

<p><b>May 21, 2008.  Version 1.2517.</b></p>

<ul type=None>
<li><p>Fixed recently introduced bug where cofr command did not work on
undisplayed selected surfaces. TG
</ul>

<p><b>May 20, 2008.  Version 1.2514.</b></p>

<ul type=None>
<li><p>Made selecting molecular surface select atoms and bonds. TG
<li><p>Made action menu set pivot work on selected surfaces. TG
<li><p>Made volume viewer detect surface color/style changes made from Actions menu or by other means. TG
</ul>

<p><b>May 19, 2008.  Version 1.2511.</b></p>

<ul type=None>
<li><p>Fixed fit map error when no atoms selected and simulated map enabled. TG
</ul>

<p><b>May 15, 2008.  Version 1.2511.</b></p>

<ul type=None>
<li><p>Made Actions / Focus menu entry work for selected surfaces. TG
<li><p>Fixed volume series error when playing series when active volume
in not in series. TG
<li><p>Fixed volume series bug undisplaying surfaces when caching off. TG
</ul>

<p><b>May 13, 2008.  Version 1.2510.</b></p>

<ul type=None>
<li><p>Made Actions menu entries work when molecular surfaces are selected.
Formerly they only worked when atoms were selected. TG
<li><p>Made selecting a surface in mesh or dot style require clicking on
a mesh line or dot.  Formerly any area of the surface could be clicked.
The new behavior allows selecting molecules within surfaces. TG
<li><p>Made volume surfaces selectable. TG
<li><p>Made Actions / Surface and Actions / Color menu entries work on
non-molecular surfaces. TG
<li><p>Removed Actions / Target menu. TG
</ul>

<p><b>May 12, 2008.  Version 1.2510.</b></p>

<ul type=None>
<li><p>Fixed crash at startup on mac when remote displaying caused by
space navigator tool. Same problem when --nogui mode used and the user
is not logged in to the mac console. TG
</ul>

<p><b>May 9, 2008.  Version 1.2510.</b></p>

<ul type=None>
<li><p>Made molecular surface calculation report the number of surface
components and the solvent excluded and solvent accessible surface areas. TG
<li><p>Fixed error in surface color tool when surface is colored by volume
value and the volume is closed and then the surface is changed. TG
</ul>

<p><b>May 8, 2008.  Version 1.2510.</b></p>

<ul type=None>
<li><p>Removed accelerators on/off menu entries from Tools / General Controls
menu and renamed Accelerators List entry to Keyboard Shortcuts.  Keyboard
shortcuts are now enabled with a switch on the dialog and that setting is now
saved in preferences automatically. TG
</ul>

<p><b>May 7, 2008.  Version 1.2510.</b></p>

<ul type=None>
<li><p>Made Fetch Structure by ID report download progress in status line. TG
</ul>

<p><b>May 6, 2008.  Version 1.2510.</b></p>

<ul type=None>
<li><p>Fixed recently introduced bug in model panel Tile button where models
were placed in random order on screen.  Fixed ordering is by model id number. TG

</ul>

<p><b>May 5, 2008.  Version 1.2510.</b></p>

<ul type=None>
<li><p>Put least used controls of surface color dialog in options panel. TG
<li><p>Made surface color dialog use a separate volume menu that is displayed
when color method is by volume data value. Formerly every volume appeared as
an entry in the coloring method menu. TG
<li><p>Added electrostatic coloring method to surface color dialog. This is
the same as coloring by volume data value, only with dialog text specialized
to save "electrostatic potential" to reduce confusion. TG
<li><p>	Fixed session saving bug with custom colored molecular surface models.
Bug introduced in past month.  TG
</ul>

<p><b>May 2, 2008.  Version 1.2510.</b></p>

<ul type=None>

<li><p>Made benchmark tool draw models on screen to avoid inflated frame rates.
Formerly drawing was done in an internal buffer and not shown and newer drivers
shortcut the rendering leading to frame rates sometimes 2x higher than in
actual use.  TG
<li><p>Added "report scores" button to benchmark tool to send scores to
RBVI for posting on web. TG
<li><p>Simplified benchmark dialog to show only the commonly used controls,
with others hidden in an options panel. TG
<li><p>Fixed bug in benchmark tool with solid rendering where volume was not
in field of view so some graphics drivers rendered nothing leading to very
large test cases which caused memory errors. TG
</ul>

<p><b>April 30, 2008.  Version 1.2508.</b></p>

<ul type=None>
<li><p>Fixed bug in crystal contacts tool where contacts between a crystal
asymmetric unit and copies translated by unit cell translations were not
detected. TG
<li><p>Added option to crystal contacts tool to create moleucule models for
contacting copies. TG
</ul>

<p><b>April 28, 2008.  Version 1.2506.</b></p>

<ul type=None>
<li><p>Made volume eraser radius slider resize when the dialog is resized. TG
</ul>

<p><b>April 25, 2008.  Version 1.2506.</b></p>

<ul type=None>
<li><p>Made model panel Tile button highlight when non-molecule models selected. TG
</ul>

<p><b>April 24, 2008.  Version 1.2506.</b></p>

<ul type=None>
<li><p>Made model panel Tile button work with all models, not just molecules. TG
</ul>

<p><b>April 18, 2008.  Version 1.2505.</b></p>

<ul type=None>
<li><p>Made phantom force feedback tool volume aligned cross-hair display
correctly when local volume coordinates are rotated. TG
</ul>

<p><b>April 17, 2008.  Version 1.2504.</b></p>

<ul type=None>
<li><p>Added color palette option menu and a button to reverse color order
to surface color tool. TG
</ul>

<p><b>April 16, 2008.  Version 1.2503.</b></p>

<ul type=None>
<li><p>Made multiscale tool with surface resolution = 0 (solvent excluded
surface) use probe radius, vertex density and disjoint component preference
settings.  Formerly it used values that could not be changed. TG
<li><p>Made relative orientation schematic shortcut "ai" not give an error
when rotation angle is zero. TG
</ul>

<p><b>April 15, 2008.  Version 1.2503.</b></p>

<ul type=None>
<li><p>Made phantom force feedback tool handle volume step change, and
made move marker warn if no marker is under cursor. TG
</ul>

<p><b>April 11, 2008.  Version 1.2503.</b></p>

<ul type=None>

<li><p>Simplified Phantom Force Feedback dialog.  Made key commands work from
main Chimera window.  Changed move models, zoom, contour level, move marker
keyboard commands to press once to activate, again to deactivate.  Formerly key
had to be held down. TG
<li><p>Included Phantom force feedback OpenHaptics event handling in Windows
Chimera distribution. User is required to install OpenHaptics driver. TG
</ul>

<p><b>April 10, 2008.  Version 1.2503.</b></p>

<ul type=None>
<li><p>Fixed bug where molecular surface calculation for zero atoms failed. TG
</ul>

<p><b>April 8, 2008.  Version 1.2503.</b></p>

<ul type=None>
<li><p>Made "ac" command accept arguments which are keyboard shortcuts to run.
Without arguments it still enables typing keyboard shortcuts to main window. TG
</ul>

<p><b>April 7, 2008.  Version 1.2503.</b></p>

<ul type=None>
<li><p>Added support for Space Navigator six degree-of-freedom input device
to Windows Chimera versions. TG
</ul>

<p><b>April 4, 2008.  Version 1.2503.</b></p>

<ul type=None>
<li><p>Made molecular surface calculation not show a console window on Windows.
TG
</ul>

<p><b>April 3, 2008.  Version 1.2503.</b></p>

<ul type=None>
<li><p>Fixed molecular surface calculation on Windows. Was interpreting ctrl-z
as end of input. Also mscalc program was not started correctly. TG
</ul>

<p><b>April 2, 2008.  Version 1.2502.</b></p>

<ul type=None>
<li><p>Added support for Space Navigator six degree-of-freedom input device
to Mac Chimera versions. TG
</ul>

<p><b>April 1, 2008.  Version 1.2502.</b></p>

<ul type=None>
<li><p>Fixed bug where enabling surface capping and surface coloring caused
continuous recalculation of cap and colors. TG

<li><p>Made surface cap color not flicker to solid color when moving cap. TG
</ul>

<p><b>March 27, 2008.  Version 1.2502.</b></p>

<ul type=None>
<li><p>Made multiscale dialog use stand-alone program molecular surface
calculation when resolution set to zero for solvent excluded surface. TG
</ul>

<p><b>March 26, 2008.  Version 1.2501.</b></p>

<ul type=None>
<li><p>Optimized surface distance calculation (keyboard shortcut "sd") by
translating Python code to C++.  Several hundred times faster.  TG
</ul>

<p><b>March 25, 2008.  Version 1.2501.</b></p>

<ul type=None>
<li><p>Changed solvent excluded/accessible surface area calculation to use
analytical values instead of approximate values calculated from the triangulated
surface (which depended on vertex density). TG
<li><p>Added per-residue solvent excluded/accessible surface area (areaSES,
areaSAS) attributes viewable with Render by Attribute tool. TG
<li><p>Added solvent excluded/accessible surface area in Reply Log
output when molecular surface is calculated.
<li><p>Made up and down arrow keys work with selected surface pieces. TG
<li><p>Fixed bug in IMOD mesh file reader where normal vectors appeared in
the surface vertex array resulting in wrong inertia calculation. TG
<li><p>Added "ra" keyboard shortcut for showing render-by-attribute dialog. TG
<li><p>Added "se" keyboard shortcut for toggling silhouette edge display. TG
<li><p>Fixed bug in surface distance calculation where distance to an
edge was used when the closest distance was actually to a vertex. TG
</ul>

<p><b>March 20, 2008.  Version 1.2501.</b></p>

<ul type=None>
<li><p>Fixed meshmol command on molecular surfaces, "truth value ambiguous"
error. TG
<li><p>Fixed error in Measure and Color Blobs, "array cannot be safely
cast to required type" on 64-bit Chimera versions. TG
<li><p>Made Color Zone, Surface Zone and Surface Color work on MSMS surface
caps. TG
</ul>

<p><b>March 18, 2008.  Version 1.2500.</b></p>

<ul type=None>
<li><p>Made Chimera calculate solvent excluded molecular surfaces using a
standalone application so crashes do not crash Chimera.  TG
<li><p>Made molecular surface calculation assign per-atom solvent excluded
surface area (areaSES) and solvent accessible surface area (areaSAS) values
that can be used with Render by Attribute dialog or the "select" command. TG
<li><p>Molecular surfaces now are implemented using SurfaceModel.  Some
new attributes of this type of model are visible in the selection and model
attribute inspector dialogs. TG
<li><p>Eliminated warning messages that appeared in the Chimera reply log
on Mac OS 10.5 about an unhandled apple event.  TG
<li><p>Changed Benchmark molecule tests to only time one molecule instead of
six.
<li><p>Fixed ribbon benchmark timing, previous scores invalid.  TG
</ul>

<p><b>March 17, 2008.  Version 1.2500.</b></p>

<ul type=None>
<li><p>Fixed a triangle template allocation bug in MSMS molecular surface
calculation reducing number of crash cases in half.  Also changed to allow
surface calculation when one atom is entirely inside of another.  TG
<li><p>Made Movie Recorder respect preference for saving POVray files. TG
<li><p>Fixed InterSurf to use new SurfaceModel Python names. TG
</ul>

<p><b>March 11, 2008.  Version 1.2500.</b></p>

<ul type=None>
<li><p>Renamed Surface_Model to SurfaceModel and changed Python method
names and attributes to eliminated underscore characters.  TG
</ul>

<p><b>March 5, 2008.  Version 1.2499.</b></p>

<ul type=None>
<li><p>Added dot surface display and dot size setting to surface models,
settable with selection inspector. TG
</ul>

<p><b>March 4, 2008.  Version 1.2498.</b></p>

<ul type=None>
<li><p>Reduced memory use of volume solid style rendering in color map
mode.  Was unnecessarily making floating point copy of map. TG
</ul>

<p><b>February 29, 2008.  Version 1.2497.</b></p>

<ul type=None>
<li><p>Removed setting to flip surface lighting normals visible in
selection inspector dialog. TG
</ul>

<p><b>February 28, 2008.  Version 1.2496.</b></p>

<ul type=None>
<li><p>Added consistency checking (valid record size) in delphi map
file reader. TG
</ul>

<p><b>February 27, 2008.  Version 1.2495.</b></p>

<ul type=None>
<li><p>Added checkbuttons to volume tracer mouse mode panel that match
those in the Mouse menu. TG
<li><p>Fixed volume tracer session restore bug where a second traced surfaces
model was created after restoring a session containing traced surfaces. TG

<li><p>Made volume tracer delete surface panel only delete selected
traced surfaces.  Was deleting any selected surface. TG
<li><p>Made volume tracer continuous marker placement while dragging
work with "on spot", "on plane", or "outside data" mouse mode.  Was ignoring
those settings and always dropping markers on plane. TG
</ul>

<p><b>February 26, 2008.  Version 1.2495.</b></p>

<ul type=None>
<li><p>Fixed volume tracer bug where traceback given if "marker color
matches volume color" enabled and marker is placed. TG
<li><p>Made crash dump detection for bug reporting work on Mac OS 10.5.
Mac OS 10.5 uses separate file for each crash, while 10.4 used one file
for all crashes of the same application. TG
</ul>

<p><b>February 22, 2008.  Version 1.2495.</b></p>

<ul type=None>
<li><p>Modified per-model clipping command to not modify existing clip
plane axis or origin unless explicit options are given. TG

</ul>

<p><b>February 21, 2008.  Version 1.2495.</b></p>

<ul type=None>
<li><p>Added option to create simulated map (uses molmap command) 
to the fit map dialog. TG
</ul>

<p><b>February 20, 2008.  Version 1.2495.</b></p>

<ul type=None>
<li><p>Added per-model clipping command mclip. TG
<li><p>Fixed volume eraser bug that gave traceback when erasing done
with eraser sphere entirely outside of volume. TG
<li><p>Fixed bug on movement mouse mode where no translation was possible
if near clip plane was at or in front of eye position.  Changed behavior
so amount of translation is based on dragging center of rotation of object.
TG
</ul>

<p><b>February 19, 2008.  Version 1.2494.</b></p>

<ul type=None>
<li><p>Added zflip option to vop (volume operation) command to change
the hand of a map by reversing the order of the z planes. TG
</ul>

<p><b>February 15, 2008.  Version 1.2493.</b></p>

<ul type=None>
<li><p>Added IMOD map file reader, file suffix ".rec". These are MRC maps
but signed 8-bit mode is interpreted as unsigned. TG
<li><p>Changed volume solid style transparency modulation from
t -&gt; t ** (1.0/planes) to t -&gt; t ** (1.0/(planes*t)). Here planes
= minimum number of planes along each axis times the transparency factor
and the initial transparency t is the height of the transfer function on
the histogram (0-1 range). For transparent voxels the change is minor.
For opaque voxels it makes the effective thickness smaller and avoids
a large brightness jump between opacity 0.99 and 1.0. TG

</ul>

<p><b>February 13, 2008.  Version 1.2493.</b></p>

<ul type=None>
<li><p>Fixed bug where deleting volume tracer links by means other than
the "delete links" menu entry would later cause session saving to fail.  TG
<li><p>Made session saving for volume opens put paths in the session file
that are relative to the session file directory if the volume data lies
within or below that directory. This allows restoring the session file after
moving a directory containing session files and volume data. TG
<li><p>Added linewidth option to shape command for meshes. TG
<li><p>Made shape command show mesh by default only for icosahedron
(not sphere) with lattice option specified. TG
<li><p>Changed shape command default color to "gray". TG
</ul>

<p><b>February 12, 2008.  Version 1.2493.</b></p>

<ul type=None>

<li><p>Added displayThreshold option to molmap command to set the initial
contour level of the new map so that the specified fraction of total mass
is contained within the contour.  Default value 0.95.  TG
<li><p>Changed effect of volume solid style transparency slider so that
it modulates transparency even when factor times depth in planes is less
than 1.  This allows making completely opaque single planes. TG
</ul>

<p><b>February 8, 2008.  Version 1.2493.</b></p>

<ul type=None>
<li><p>Reduced memory use when saving a volume zone. For maps larger than
16 Mvoxels the map mask is computed plane by plane.  Smaller maps use 12
bytes per voxel overhead.  TG
</ul>

<p><b>February 7, 2008.  Version 1.2493.</b></p>

<ul type=None>
<li><p>Fixed split map button in color zone dialog. TG
</ul>

<p><b>January 31, 2008.  Version 1.2492.</b></p>

<ul type=None>
<li><p>Combined "fit model in map" and "fit map in map" dialogs into a single
dialog, and combined menu entries into one entry.  Dialog has new layout but
same functionality as original two dialogs. TG
<li><p>Added option for real-time updating of correlation and average map
value to fit map dialog. TG
</ul>

<p><b>January 30, 2008.  Version 1.2486.</b></p>

<ul type=None>
<li><p>Added ability to create surfaces from stacks of loops and curves
with the volume path tracer tool.  Uses the new Surface panel of the volume
path tracer dialog. TG
<li><p>Renamed "volume path tracer" to "volume tracer".  TG
<li><p>Reordered volume tools menu to put more frequently useful tools near
the top and group them by functionality. TG
<li><p>Added split map button to color zone dialog and eliminated separate
volume tools menu entry for split map. TG

<li><p>Changed molmap ratio of resolution to Gaussian standard deviation
to be 1/(pi*sqrt(2)) (~0.225) from former value of 1/(2*sqrt(pi)) (~0.282). TG
<li>Made split map by color zone give proper alignment when map coordinates
involve a rotation.
</ul>

<p><b>January 29, 2008.  Version 1.2485.</b></p>

<ul type=None>
<li><p>Added keyboard shortcut "or" to toggle orthographic projection. TG
</ul>

<p><b>January 25, 2008.  Version 1.2485.</b></p>

<ul type=None>
<li><p>Added ability to export surfaces in Wavefront OBJ format using
File / Export Scene.  TG
<li><p>Optimized "split map by color zone" to use less memory.  Operates
plane by plane for maps larger than 16 Mvoxels.  TG

<li><p>Added mouse mode to resize a selected surface by dragging.  Enabled
for one drag use by keyboard shortcut sz.  TG
<li><p>Added keyboard shortcut "ao" to activate only selected surfaces. TG
<li><p>Added keyboard shortcut "oc" to allow typing one command and then
automatically return to entering keyboard shortcuts. TG
<li><p>Allowed resizing volume path tracer markers by dragging the mouse
while holding the Alt key down if the move/resize mode is enabled. TG
</ul>

<p><b>January 24, 2008.  Version 1.2485.</b></p>

<ul type=None>
<li><p>Added "resample" operation to vop command to resample one volume
data set on the grid of a second volume data set.  TG
</ul>

<p><b>January 23, 2008.  Version 1.2485.</b></p>

<ul type=None>

<li><p>Fixed incorrect rainbow colormap direction for volumes with
rotated local coordinates. TG
<li><p>Made "measure and color blobs" dialog and mask command ignore
outline boxes around volume data. TG
<li><p>Added "shape" command that makes surfaces having standard geometric
shapes.  Handles cylinder, sphere, and icosahedron.  Includes icosahedral
mesh capabilities of hkcage command.  Includes interpolating icosahedron
with sphere and alternate coordinates systems as in the Icosahedron surface
dialog. TG
<li><p>Changed vm keyboard shortcut to mask active volume using selected
surfaces.  Formerly it masked volume using volume contour surface.  TG
</ul>

<p><b>January 22, 2008.  Version 1.2485.</b></p>

<ul type=None>
<li><p>Made volume contour surfaces have correct lighting when the voxel
size along an axis is made negative to flip the hand of the map.  Formerly
two sided lighting gave dark surface in this case. TG
<li><p>Made image stack volume reader handle multi-page tiff images. TG
<li><p>Fixed surface capping bug when new surface created while capping is
enabled.  TG
</ul>

<p><b>January 18, 2008.  Version 1.2485.</b></p>

<ul type=None>
<li><p>Added molmap command to make volume from a molecule by summing
Gaussians at each atom position. TG
</ul>

<p><b>January 16, 2008.  Version 1.2483.</b></p>

<ul type=None>
<li><p>Made opening tiff image stacks work by selecting all images in the
open dialog.  Formerly only one image was selected and others that had the
same prefix and different numeric suffix were inferred. TG
<li><p>Made image stack reader handle image types other than TIFF.  Can
handle any image format understood by the Python image library (e.g. png,
jpeg). TG
</ul>

<p><b>January 15, 2008.  Version 1.2483.</b></p>

<ul type=None>

<li><p>Fixed chimera "--send" startup option on mac.  Was always starting
a new instance of chimera. TG
</ul>

<p><b>January 11, 2008.  Version 1.2483.</b></p>

<ul type=None>
<li><p>Removed marker set models closed with the file menu entry in
the volume path tracer dialog.  Formerly the models were just emptied
of markers. TG
<li><p>Changed mask command sandwich option default value to true. TG
<li><p>Changed mask command fullmap option to require a true/false value.
Formerly the option took no value. TG
</ul>

<p><b>January 10, 2008.  Version 1.2483.</b></p>

<ul type=None>
<li><p>Made default projection axis for mask command y instead of z. TG

<li><p>Renamed "pick surface pieces" dialog and menu entry to the more
descriptive "measure and color blobs". TG
<li><p>Added slab option to mask command to mask using a slab of specified
thickness created by thickening a surface. TG
</ul>

<p><b>January 9, 2008.  Version 1.2483.</b></p>

<ul type=None>
<li><p>Added selection inspector attributes for surface pieces:
surface piece count, line thickness, line smoothing, lighting, two
sided lighting, lighting normal direction, transparency brightness. TG
<li><p>Made selection inspector attributes for surface models and pieces
update when changed using other dialogs or commands. TG
</ul>

<p><b>January 8, 2008.  Version 1.2481.</b></p>

<ul type=None>
<li><p>Added attributes to selection inspector dialog for surfaces and
surface pieces.  Attributes: color, display style (mesh/solid), displayed,
triangle count, active, selectable with mouse.  TG

<li><p>Made selected surfaces show green outline even when "selectable with
mouse" is turned off.  TG
<li><p>Made keyboard shortcuts work on surfaces selected with select command.
The select command selects the surface model but not the surface components.
TG
</ul>

<p><b>January 7, 2008.  Version 1.2481.</b></p>

<ul type=None>
<li><p>Made surfnet tool create a surface model instead of a vrml model.
Allows measuring enclosed volume, coloring, splitting disjoint components,
....  TG
<li><p>Eliminated _cubes contour calculation module.  TG
</ul>

<p><b>January 2, 2008.  Version 1.2481.</b></p>

<ul type=None>
<li><p>Added fill value option to vop command.  Large negative fill values
can produce flat cut faces when erasing an octant.  TG

</ul>

<p><b>December 21, 2007.  Version 1.2480.</b></p>

<ul type=None>
<li><p>Made help command show documentation for commands volume, topo, sym,
bondzone, split, msc, meshmol, mask, hkcage, crystalcontacts.  TG
<li><p>Added vop (volume operation command) to erase an octant.  Plan to
support many other volume modifying operations (gaussian filter, erase
outside sphere, interpolate, ...) as options to this command in the future.
TG
<li><p>Changed volume suffixes from <N> format (e.g. "map.mrc <1>")
to instead append model id number.  Previous suffix number was not the
model id number.  TG
</ul>

<p><b>December 20, 2007.  Version 1.2480.</b></p>

<ul type=None>
<li><p>Made meshmol command work when surface has the same model id number
as an existing molecule.  TG
<li><p>Fixed bug in multiscale tool where molecule copies were not closed
when multiscale model deleted.  TG
</ul>

<p><b>December 18, 2007.  Version 1.2479.</b></p>

<ul type=None>
<li><p>Made changing volume step size with step menu not turn off automatic
step size adjustment.  Now the voxel limit for automatic step adjustment is
instead changed to the number of voxels shown with the chosen step.  TG
<li><p>Changed default volume solid threshold brightness at 99% rank data
value from 1.0 to 0.99 to avoid completely opaque voxels.  TG
<li><p>Reduced memory allocation used to zero volume solid 3-d texture from
4*(number of voxels) bytes to 4*(number of voxels in one xy plane).  TG
<li><p>Optimized pick surface piece tool.  About 10x faster in typical case.
TG
<li><p>Added Tools / Volume Data menu entry that adds Volume menu to main
window menu bar, and remembers this setting for future sessions.  TG
</ul>

<p><b>December 14, 2007.  Version 1.2476.</b></p>

<ul type=None>
<li><p>Fixed toggle surface selectability keyboard shortcut ts.  TG
</ul>

<p><b>December 12, 2007.  Version 1.2476.</b></p>

<ul type=None>
<li><p>Made topography command work with yz and xz planes.  Formerly only
handled xy planes.  TG
<li><p>Added topography command "replace" option to replace the existing
topography surface rather than create a new one.  TG
<li><p>Made volume planes show the correct depth after All planes button is
pressed when step size is greater than 1.  TG
<li><p>Fixed volume command writing brix, mrc and netcdf formats.
Was giving an error message and not writing file. TG
</ul>

<p><b>December 11, 2007.  Version 1.2476.</b></p>

<ul type=None>
<li><p>Made volume solid rendering model have same id number as volume
surface model.  Wasn't doing that when solid was shown first.  TG
</ul>

<p><b>December 7, 2007.  Version 1.2476.</b></p>

<ul type=None>
<li>Fixed bug where volume data set menu and list box contained deleted
volumes. TG
<li><p>Fixed error in session restore where multiscale models of volume
path tracer marker sets were present.  TG
</ul>

<p><b>December 5, 2007.  Version 1.2476.</b></p>

<ul type=None>

<li><p>Removed checkbutton volume planes panel of volume dialog and added
"one", "all" buttons to control display of single plane or all planes.
New interface makes it clearer that plane display is not a mode, and makes
display of all planes more reliable. TG
<li><p>Made sessions include derived maps (e.g. Gaussian filter) that have
been saved to a separate volume file. TG
</ul>

<p><b>December 4, 2007.  Version 1.2476.</b></p>

<ul type=None>
<li><p>Fixed bug that caused volume histogram to be off by a few percent
in number of voxels counts per value bin.  TG
<li><p>Added threshold normalization to morph map dialog.  Adjusts volume
threshold to keep a fixed number of grid points within the contour surface
for all interpolated maps.  TG
</ul>

<p><b>November 30, 2007.  Version 1.2475.</b></p>

<ul type=None>
<li><p>Added key shortcuts to create a new volume using the zone display of
the active volume (zv), and the region outside the zone (ez, erase zone). TG

</ul>

<p><b>November 29, 2007.  Version 1.2475.</b></p>

<ul type=None>
<li><p>Added topography command which creates a surface corresponding to
a volume data plane.  The surface height above the volume plane is
proportional to the volume data value.  TG
</ul>

<p><b>November 27, 2007.  Version 1.2473.</b></p>

<ul type=None>
<li><p>Made Chimera compatible with 2 year old Chimera 1.2154 preferences files.
Showing volume with new Chimera and old preferences file caused error.  TG
<li><p>Made restoring a session that uses the Surface Color tool not display
the Surface Color dialog unless it was displayed when the session was saved.
TG
<li><p>Added TIFF volume file reader support for 16-bit unsigned integer,
32 bit floating point, and 32 bit integer pixel values.  TG
<li><p>Added volume file writing in BRIX  format (used by crystallography
program O). TG

</ul>

<p><b>November 15, 2007.  Version 1.2470.</b></p>

<ul type=None>
<li><p>Chimera production release 1.2470.
</ul>

<p><b>November 13, 2007.  Version 1.2469.</b></p>

<ul type=None>
<li><p>Made Gaussian filter copy the local coordinate rotation of original
map. TG
<li><p>Made volume subregion resampling pad by half a voxel between the
displayed outline box and the resampling grid.  This allows resampling on
the exact grid of a second map by clicking outside that map to outline it
(which includes a half voxel padding).  TG
<li><p>Added display full volume keyboard shortcut fv.  Useful after
showing a subregion for returning to full map display.  TG
</ul>

<p><b>November 8, 2007.  Version 1.2468.</b></p>

<ul type=None>
<li><p>Fixed priism volume file reader byte order detection code.  Did
not work correctly with 8-bit data values.  TG
</ul>

<p><b>November 7, 2007.  Version 1.2468.</b></p>

<ul type=None>
<li><p>Added options to the Gaussian filter dialog to use only the displayed
subsampling, and to use only the displayed subregion. TG
<li><p>Fixed volume caching bug that sometimes caused single plane volume
data display to be blank.  TG
<li><p>Fixed bug in morph map where the first map was modified instead of
creating a new interpolated map when the first map was writable. TG
</ul>

<p><b>November 6, 2007.  Version 1.2468.</b></p>

<ul type=None>
<li><p>Made Chimera start correctly on Mac OS 10.5 (Leopard) by preventing
Chimera from trying to automatically start the X server, since that is now
done by the operating system.  TG
<li><p>Fixed bug in error message displayed when reading truncated XPLOR
volume files.  TG
</ul>

<p><b>November 5, 2007.  Version 1.2468.</b></p>

<ul type=None>
<li><p>Made BRIX/DSN6 (O map) volume file reader apply scale and shift from
file header to 8-bit values to produce floating point values.  TG
</ul>

<p><b>October 31, 2007.  Version 1.2467.</b></p>

<ul type=None>
<li><p>Made mask command handle degenerate cases where projected grid lines
exactly intersect surface vertices or edges.  TG
</ul>

<p><b>October 29, 2007.  Version 1.2466.</b></p>

<ul type=None>
<li><p>Added "sandwich" option to mask command for extracting the volume
between two surfaces along a projection axis.  Without this option regions
between one surface and the volume box boundary are also included.  TG
</ul>

<p><b>October 26, 2007.  Version 1.2466.</b></p>

<ul type=None>
<li><p>Changed hkcage command which makes icosahedral cages use keyword
options instead of requiring options to be in fixed order.  Added "replace"
keyword option to replace the existing cage instead of creating a new model.
TG

</ul>

<p><b>October 24, 2007.  Version 1.2465.</b></p>

<ul type=None>
<li><p>Made MRC volume files written by Chimera contain the Chimera version
and date. TG
<li><p>Made split command which places chains of an atomic model in separate
models do nothing when applied to a single chain. TG
</ul>

<p><b>October 23, 2007.  Version 1.2465.</b></p>

<ul type=None>
<li><p>Added mask command which creates a volume data set containing
only the values within a surface. TG
<li><p>Fixed bug in close points calculation used by Find Clashes,
Color Zone and Surface Zone tools which in rare cases may have led to
incorrect neighbor calculation or hanging. TG
</ul>

<p><b>October 22, 2007.  Version 1.2465.</b></p>

<ul type=None>
<li><p>Fixed bug where meshmol command would create a model aligned
with the model with lowest id number instead of the original mesh model. TG
<li><p>Fixed bug where resampled volume had no name in volume dialog and
model panel. TG
<li><p>Made volume display tolerate externally deleted contour surface groups,
for example with Ds keyboard shortcut. TG
</ul>

<p><b>October 18, 2007.  Version 1.2463.</b></p>

<ul type=None>
<li><p>Fixed volume series bug opening priism format data. TG
</ul>

<p><b>October 17, 2007.  Version 1.2463.</b></p>

<ul type=None>
<li><p>Made morph map volume browse button display the opened data. TG
</ul>

<p><b>October 11, 2007.  Version 1.2458.</b></p>

<ul type=None>
<li><p>Made calculation of volume enclosed in a surface handle surface holes
but placing a point at the center of each boundary curve and making a triangle
fan to cover the hole. TG
<li><p>Add split map and fourier transform menu entries (Tools / Volume Data).
TG
</ul>

<p><b>October 10, 2007.  Version 1.2456.</b></p>

<ul type=None>
<li><p>Added several tools from experimental features web page to the
distribution: morph map, transform molecule coordinates, mesh to molecule,
icosahedral cage (hkcage command), surface distance, crystal contacts, volume
series, movement mouse mode, flatten icosahedron, split molecule, multiscale
color command, pick surface pieces, symmetry copies command (sym).  TG
<li><p>Added Tools menu to volume dialog. TG
<li><p>Optimized speed of Find Clashes tool. TG
<li><p>Added version number to Chimera HDF map file format. TG
</ul>

<p><b>October 9, 2007.  Version 1.2455.</b></p>

<ul type=None>
<li><p>Added "cap high values at box faces" volume surface rendering option. TG
<li><p>Made popup balloons for IMOD object surfaces give object name.
Mousing over other selectable surfaces will also show names.  TG
<li>Add keyboard shortcut Ds to delete selected surfaces and Sc to split
selected surfaces into one surface for each connected component. TG
</ul>

<p><b>October 6, 2007.  Version 1.2454.</b></p>

<ul type=None>
<li><p>Made volume contour surfaces use lighting normals parallel to data
gradient instead of averaged surface triangle normals.  Gives less faceted
apperance.  TG
<li><p>Made multiscale model tool use surface lighting normals based on
gradient of atom density rather than average normal of surface triangles.
Small improvement in surface smoothness.  TG
</ul>

<p><b>October 5, 2007.  Version 1.2454.</b></p>

<ul type=None>
<li><p>Added IMOD mesh file reader. TG
<li><p>Added Gaussian filter tool to smooth volume data by convolving with
a gaussian. TG
<li><p>Added Fourier transform keyboard shortcut FT to display 3-dimensional
Fourier transform of volume data. TG
<li><p>Added keyboard shortcut sm to split a volume data set into multiple
data sets, one for each color of the original volume, as colored by the
color zone tool. TG
<li><p>Made multiscale model tool not change the display style of the original
molecule used in building multimeric assembly.  Only displays new copies as
surfaces.  TG

</ul>

<p><b>October 4, 2007.  Version 1.2454.</b></p>

<ul type=None>
<li><p>Made surface capping not show a cap for a clipped unit cell outline box.
(Bug 4605). TG
<li><p>Made unit cell tool pack asymmetric unit in single unit cell even when
molecule atoms/ribbon is undisplayed (as when using Multiscale).  Now uses
center of all atoms rather than center of displayed atoms for packing.
(Bug 4606). TG
</ul>

<p><b>October 3, 2007.  Version 1.2454.</b></p>

<ul type=None>
<li><p>Added tool to print mean, standard deviation and RMS for volume data
(Tools / Volume Data / Volume Mean, SD, RMS). TG
<li><p>Made color zone slider range equal to diagonal size of surface bounding
box.  Formerly maximum slider value was always 30.  TG
<li><p>Made surface capping not create a cap for clipped volume outline box. TG

</ul>

<p><b>October 2, 2007.  Version 1.2451.</b></p>

<ul type=None>
<li><p>Made volume contour surfaces cover volume box faces where high
density is exposed.  TG
</ul>

<p><b>September 26, 2007.  Version 1.2450.</b></p>

<ul type=None>
<li><p>Made volume contour calculation work on volumes up to size 4 Gvoxels.
Formerly the limit was 4/3 Gvoxels.  TG
</ul>

<p><b>September 20, 2007.  Version 1.2448.</b></p>

<ul type=None>
<li><p>Added series of 10 initial volume colors to volume data display
options panel.  Opened data sets are shown in different colors.  TG
</ul>

<p><b>September 19, 2007.  Version 1.2448.</b></p>

<ul type=None>
<li><p>Made volume data saving use a temporary file if map is written back
over itself.  Formerly this would cause an error if the map was not entirely
cached in memory because the source file would be erased before all the
needed data was obtained.  TG
</ul>

<p><b>September 18, 2007.  Version 1.2448.</b></p>

<ul type=None>
<li><p>Added "compress" option to volume command to compress data when
saving in Chimera map format.  Useful for mask files.  TG

<li><p>Made volume command region option accept "all" or "full" value
to set region display to show the full data set.  TG
<li><p>Fixed bug where volume command did not accept upper case boolean values
True, TRUE, False, .... TG
<li><p>Fixed volume command so that model id numbers of "solid" models can
be used.  Formerly the model id of the volume surface model was required.  TG
<li><p>Made default solid volume rendering thresholds use only 2 nodes for
mask data sets having just two values 0/1.  TG
<li><p>Made Chimera map file include original file names with suffix stripped
off when multiple maps are written to one file.  TG
</ul>

<p><b>September 17, 2007.  Version 1.2448.</b></p>

<ul type=None>
<li><p>Added "symmetry" option to volume command that assigns symmetry
matrices to a volume data set.  It takes an argument "icos,XXX" where XXX
is one of 222, 2n5, n25, 2n3, 222r, 2n5r, n25r, 2n3r to specify icosahedral
symmetry in one of the standard coordinate frames as in the icosahedron
tool.  Future additions will support space and point group and screw symmetries
and BIOMT PDB matrices.  TG
</ul>

<p><b>September 15, 2007.  Version 1.2448.</b></p>

<ul type=None>
<li><p>Made experimental "sym" command use symmetries associated with volume
data set.  If there are none it uses BIOMT matrices from PDB model as
previously.  Not yet on web. TG
<li><p>Added "contact" and "range" options to "sym" command to make molecule
copies only when it is near the original copy.  Both parameters take a
distance.  Contact requires a pair of atoms within the threshold distance
while range requires the center of the molecule bounding boxes to be within
the specified range.  Not yet on web. TG
<li>Added keyboard shortcut "ic" to assign icosahedral 222 symmetry to the
active volume data set. TG
</ul>

<p><b>September 12, 2007.  Version 1.2446.</b></p>

<ul type=None>
<li><p>Added volume command chunkShape option for writing map files that
allow fast access to yz planes.  TG
</ul>

<p><b>September 11, 2007.  Version 1.2445.</b></p>

<ul type=None>

<li><p>Made CCP4 and MRC separate file formats in File / Open dialog.
Formerly they were treated as one format.  CCP4 reader now will not
incorrectly interpret xorigin, yorigin, zorigin parameters found only
in MRC2000 files.  TG
<li><p>Changed CCP4 and MRC file readers heuristic for deciding whether
origin header values (ncstart, nrstart, nsstart) are valid.  Now requires
that they have magnitude no larger than 10 times the maximum data size along
the 3 axes.  Formerly use limit of 1 times original axis data size for each
axis.  Fixes bug 4473. TG
<li><p>Replaced HDF file reader with two file readers that use HDF: 1) EMAN HDF
and 2) Chimera map format.  TG
<li><p>Added Chimera map file writer.
<li><p>Made movie recorder encode from jpeg images.  Fixes bug 4284.  TG
<li><p>Made surface color properly handle volume data set that is closed
while it is being used for automatic color updates.  TG
</ul>

<p><b>September 10, 2007.  Version 1.2445.</b></p>

<ul type=None>
<li><p>Clamped colormap size for solid rendering of volumes to maximum
reported by OpenGL.  Fixed bug 4324. TG
<li><p>Fixed volume path tracer bug where adding third marker set sometimes
caused dialog to go into infinite resizing loop adding and removing a
scrollbar.  Fixes bug 3305. TG
</ul>

<p><b>September 7, 2007.  Version 1.2445.</b></p>

<ul type=None>
<li><p>Made opening volume data set with a Chimera command or on the Chimera
command-line give a explanatory error message instead of a Python traceback.
Fixes bug 4450. TG
</ul>

<p><b>September 5, 2007.  Version 1.2445.</b></p>

<ul type=None>
<li><p>Made volume command keywords not have underscores, and not be
case sensitive, and allow unique prefix abbreviations. TG
<li><p>Made volume command color
options accept values "colorpanel", "fromeditor", or "editor" in which
case color is taken from color dialog.  Also can now use color names
defined with Chimera colordef command. TG
<li><p>Made volume command save path option accept
"browse" or "browser" in which case a modal save file dialog is opened
to choose the file. TG
<li><p>Fixed bug saving sessions when volume dialog shown but no volumes
are opened. TG
<li><p>Made volume crop button use a circumscribing data axis aligned box
when selection box has been rotated.  TG
</ul>

<p><b>September 4, 2007.  Version 1.2443.</b></p>

<ul type=None>
<li><p>Added subregion selection panel controls to copy subregions that
are not aligned with the data axes.  New controls are "rotate selection box"
switch, "resample voxel size" entry, and "resample" button. TG
<li><p>Made mrc, netcdf and hdf file reader and writer code save and
restore data rotation. TG
<li><p>Made solid style volume rendering correctly display skewed data,
common with crystallographic density maps. TG
<li><p>Eliminated "double" and "half" button on subregion selection panel
to reduce crowding.  Rarely used. TG
<li><p>Allow unicode volume files names. Fixes bug 4433. TG
</ul>

<p><b>August 24, 2007.  Version 1.2442.</b></p>

<ul type=None>
<li><p>Added "volume" command to change all rendering settings of volume
data, that can be changed with the volume dialog. TG
<li><p>Made volume object a subclass of surface model.  This allows
extension code to more easily obtain the volume object from the list
of open models with chimera.openModels.list(). TG
</ul>

<p><b>August 23, 2007.  Version 1.2441.</b></p>

<ul type=None>
<li><p>Changed volume code so that Chimera "open" command can assign model
id numbers when opening volume data. TG
<li><p>Simplified volume data python interface so extensions do not need
to use volume viewer dialog. TG
</ul>

<p><b>August 10, 2007.  Version 1.2437.</b></p>

<ul type=None>
<li><p>Made volume dialog display histograms for multiple data sets.
A single line above each histogram shows the data name, size, step menu,
visibility (eye icon) and close map button (dash icon).  Up to 3 histograms
are shown, and this limit can be changed with a new display options setting.
The "active" data set has a white background behind its name.  The level
entry field and color button and rendering options shown in the dialog
effect only the active data set.  There is no provision for changing the
settings for multiple data sets at the same time. TG
<li><p>Removed Show and Unshow buttons from bottom of dialog.  Replaced
by "eye" icon button above each data histogram to show/unshow data.
Eye icon has white background when data is shown. TG
<li><p>Eliminated data menu panel which also showed data size and step.  Added a
Data menu to the dialog menu bar.  The size and step is now shown above each
histogram. TG
<li><p>Moved display style panel (surface/mesh/solid) below histograms.  Formerly
it was above histograms.  Better to put the most useful data sets info at
the top.  Display style is now closer to color and threshold settings. TG

<li><p>Changed display stye heading from "Show: *surface  *mesh  *solid" to
"Style: *surface  *mesh  *solid".
<li><p>Fixed newly introduced bug in UHBD volume file reader.  TG
</ul>

<p><b>August 9, 2007.  Version 1.2436.</b></p>

<ul type=None>
<li><p>Made volume data size show as a single number with superscript 3
if size is the same along all three axes. TG
<li><p>Made moving volume plane slider or changing plane axis not automatically
activate plane display.  Avoids unintended switch into plane mode. TG
<li><p>Made sample grid points always have indices that are multiples of
step size.  Formerly if a volume subregion had an origin that was not a
multiple of the step size then the sample point included that origin.
This change makes precomputed subsamples behave the same way as
subsamples extracted from full resolution arrays. TG
</ul>

<p><b>August 8, 2007.  Version 1.2436.</b></p>

<ul type=None>

<li><p>Made volume plane display checkbutton update when volume region
changed using other interfaces such as subregion selection "Full"
button. TG
<li><p>Made volume dialog File / Open map dialog close as soon as file
is chosen.  Formerly it waited to see if the open succeeded.  TG
</ul>

<p><b>August 6, 2007.  Version 1.2434.</b></p>

<ul type=None>
<li><p>Made volume plane display to respect auto step size adjustment to
achieve the user-requested voxel limit.  Formerly plane display did not adjust
the step size. TG
<li><p>Fixed newly introduce volume data caching bug seen when requested
data and cache data have different origins and step sizes. TG
</ul>

<p><b>August 3, 2007.  Version 1.2434.</b></p>

<ul type=None>
<li><p>Added volume file reader for HDF5 format used by EMAN and SPARX. TG

<li><p>Added third party HDF5 library and PyTables 2.0 python module
(interface to hdf5) to the Chimera distribution. TG
</ul>

<p><b>August 2, 2007.  Version 1.2434.</b></p>

<ul type=None>
<li><p>Changed volume solid rendering transparency so that voxel brightness
is now multiplied by opacity.  This makes more transparent voxels dimmer.
This mode is now the default.  The former mode can be enabled by turning off
the new "Dim transparent voxels" setting under "Solid rendering options". TG
<li><p>Changed the effect of the transparency slider for solid volume
rendering.  It now is a fraction of displayed data thickness while formerly
it was a thickness value.  The fraction times the number of planes (minimum
for 3 axes) gives a depth in planes that is used as an exponent to modulate
transparency.  Transfer function (1-alpha) is mapped to (1-alpha)**(1/planes).
If the planes values is 2 this means that the new transparency will require
2 planes to block as much light as the same amount of light as one plane
using the unmodified transfer function. TG
<li>Changed default solid rendering transfer function ramp.  Now
starts at rank 10% data value ramping up to full brightness at rank
99% and continuing to the maximum data value at full brightness.
With new default transparency mode this provides reasonable
brightness views of single planes or full maps. TG
<li><p>Renamed volume viewer "Transparency Factor" (surface rendering) and
"Transparency Depth" (solid rendering) slider headings to "Transparency". TG
</ul>

<p><b>July 31, 2007.  Version 1.2430.</b></p>

<ul type=None>

<li><p>Made reading volume data with step size greater than 1 only allocate
space for the subsampled data.  Formerly the full size data set would be
read into memory.  The new behavior permits display of data sets larger than
will fit in memory. TG
<li><p>Made reading binary volume files report progress every 0.2 seconds
or every data z plane read, which ever is longer.  Previously used a less
reliable estimate for frequency of messages based on bytes of data read.  TG
<li><p>Fixed bug where scale bar value-changed callback occurs when scale
limits are updated if the old scale value does not lie within the limits.
Observed for volume z plane slider when switching between data sets. TG
</ul>

<p><b>July 27, 2007.  Version 1.2430.</b></p>

<ul type=None>
<li><p>Made movie recorder turn off raytrace preview overriding the
user preference. TG
<li><p>Made "movie encode" command implicitly do a "movie stop" before
encoding.  Formerly, frame capture continued while encoding was done.  TG
</ul>

<p><b>July 26, 2007.  Version 1.2430.</b></p>

<ul type=None>

<li><p>Added z plane panel to volume viewer.  Allows quick switching between
individual data z planes shown using solid rendering by moving a slider. TG
<li><p>Added volume viewer option to initially display a single z plane when
opening data sets larger than 256 Mvoxels. TG
</ul>

<p><b>July 25, 2007.  Version 1.2430.</b></p>

<ul type=None>
<li><p>Made volume dialog not transiently resize when displayed for the first
time. TG
<li><p>Made volume "show data when opened if smaller than X Mvoxels" use
size of subsampled data if a precomputed subsample file is being read. TG
</ul>

<p><b>July 24, 2007.  Version 1.2430.</b></p>

<ul type=None>
<li><p>Made volume step size menu add entries for new step sizes that are
entered using the region bounds panel. TG

<li><p>Made volume region bounds panel not deactivate auto-step adjustment
when new bounds are entered by step values are left the same.  TG
<li><p>Added user-friendly error message when allocating an array for
reading a volume data set fails.  TG
</ul>

<p><b>July 23, 2007.  Version 1.2430.</b></p>

<ul type=None>
<li><p>Made each volume have its own auto-adjust step size setting.  Formerly
all volumes used the dialog setting. TG
<li><p>Made newly opened volumes use the default rendering options instead
of the options currently set in the volume dialog. Definitely want this
behavior for auto-adjust step, but no so clear for smoothing, outline box,
others. TG
<li><p>Fixed bug where canceling volume file read disabled updates of volume
display when threshold or step size changed. TG
</ul>

<p><b>July 21, 2007.  Version 1.2430.</b></p>

<ul type=None>

<li><p>Added volume file reader for stacks of TIFF images. TG
<li><p>Added progress report status-line messages when reading volume files.
<li><p>Added cancel link (in blue) in volume progress status messages. TG
<li><p>Added support for multi-color status-line messages and detecting
mouse clicks on parts of status-line messages. TG
<li><p>Made writing MRC or NetCDF volume file read and write one z-plane
at a time to allow writing files larger than can fit in memory. TG
<li><p>Changed volume viewer dialog "step" menu entries to be just a single
number instead of 3 numbers if steps along all 3 axes are the same
(e.g. 2 instead of 2 2 2). TG
<li><p>Eliminated parentheses around volume size shown in volume dialog. TG
<li><p>Eliminated "ctrl-click on histogram to add or delete thresholds" message
from volume dialog.  Not worth the dialog space.  TG
<li><p>Multi-component volume data files are now appear as separate data sets
for each component.  This effects multi-wavelength optical microscopy files
in Priism format.  One histogram is displayed in the volume dialog instead
of multiple histograms. TG
</ul>

<p><b>July 17, 2007.  Version 1.2430.</b></p>

<ul type=None>
<li><p>Fixed movie recorder bug when using raytracing and encoding with
"play forward and backward".  GNAT 4208. TG
</ul>

<p><b>July 7, 2007.  Version 1.2425.</b></p>

<ul type=None>
<li><p>Made single plane volume data sets display using "solid" rendering
style even if dialog is set to surface or mesh.  Helpful for looking at EM
micrographs. TG
</ul>

<p><b>July 2, 2007.  Version 1.2425.</b></p>

<ul type=None>
<li><p>Made volume and multiscale surface models allow variable thickness
silhouette edges. TG
</ul>

<p><b>June 1, 2007.  Version 1.2417.</b></p>

<ul type=None>
<li><p>Fixed volume path tracer marker placement when per-model clipping
and solid rendering used.  Was ignoring per-model clip plane. TG
<li><p>Made volume path tracer marker placement with solid rendering use
threshold level given by the lowest node in the solid transfer function
with brightness > 0.  Formerly was using surface threshold. TG
<li><p>Made volume gOpenMol file reader provide a user-friendly error
message when reading an empty file.  GNAT 3952.  TG
</ul>

<p><b>May 24, 2007.  Version 1.2416.</b></p>

<ul type=None>
<li><p>Fixed volume path tracer test suite test.  Use of deprecated Python
os.tmpnam() on Windows Vista gave unwritable file.  TG
</ul>

<p><b>May 17, 2007.  Version 1.2412.</b></p>

<ul type=None>
<li><p>Fixed mesh benchmark divide by zero that occured with defective
graphics driver that could not render mesh. TG
</ul>

<p><b>May 15, 2007.  Version 1.2411.</b></p>

<ul type=None>
<li><p>Fixed 64-bit Linux dependency on system lapack / blas libraries. TG
</ul>

<p><b>May 14, 2007.  Version 1.2410.</b></p>

<ul type=None>
<li><p>Fixed movie command bug where (unnecessary) movie reset command
issued after movie encode command which was still working in background.
GNAT 3873.  TG
</ul>

<p><b>May 9, 2007.  Experimental feature.</b></p>

<ul type=None>
<li><p>Enhanced IMOD segmentation file reader to read contours and points,
creating a volume path tracer model. TG
</ul>

<p><b>May 8, 2007.  Version 1.2399.</b></p>

<ul type=None>
<li><p>Made closing volume path tracer dialog turn off the marker placement
mouse mode.  Reshowing the dialog turns the mouse mode back on. TG
<li><p>Renamed button on movie recorder output path browse dialog
from Save to Set Movie Path.  Bug #2270. TG
<li><p>Fixed bug #3833 where volume menu it fit map in map tool did not update
after a volume was closed.  Made volume menus in fit map, values at atom
positions, and morph map dialog automatically update as soon as a volume data
set is opened or closed. TG
</ul>

<p><b>May 1, 2007.  Version 1.2392.</b></p>

<ul type=None>
<li><p>Fixed bug in bondzone command where "if array:" construct used to
test if array is non-empty.  Bug introduced with switch from Numeric to
Numpy library.  TG
</ul>

<p><b>April 30, 2007.  Version 1.2388.</b></p>

<ul type=None>
<li><p>Fixed bug opening biological unit model from PQS database using
id on command-line (e.g. "open pqsID:104l") TG
</ul>

<p><b>April 27, 2007.  Version 1.2388.</b></p>

<ul type=None>
<li><p>Added code to check the Mac Python crash log to see if the last
invocation of Chimera ended in a crash.  If so, a dialog appears the next
time they run Chimera allowing them to report the crash including the
crash log. TG
<li><p>Added xray fo-fc difference maps from the Uppsala Electron
Density Server to File / Fetch by Id. TG
<li><p>Added biological unit PDB files from the Probably Quaternary Structure
(PQS) server to File / Fetch by Id. TG
</ul>

<p><b>April 26, 2007.  Version 1.2388.</b></p>

<ul type=None>
<li><p>Fixed bug #3808 where movie recorder "play forward then backward"
option caused error on Windows. TG
<li><p>Fixed bug #3812 where default movie recorder output movie file location
is unwritable on Windows Vista. TG
</ul>

<p><b>April 25, 2007.  Version 1.2384.</b></p>

<ul type=None>
<li><p>Made opening APBS, DelPhi, or UBHD electrostatic potential files
show surface color dialog instead of volume viewer. TG
</ul>

<p><b>April 11, 2007.  Version 1.2375.</b></p>

<ul type=None>
<li><p>Changed movie recorder default image file format to PPM.  Typically 3x faster image capture than with PNG image format, probably because of time spent compressing image. TG
<li><p>Bug fix.  Nucleic acid blobs reschains.py error when scale bar shown. TG
<li><p>Bug #3775 fixed.  Fit model in map when map not shown. TG
</ul>

<p><b>April 9, 2007.  Version 1.2373.</b></p>

<ul type=None>

<li><p>Added button to movie recorder to show raytracing preferences. TG
<li><p>Suppressed image saving status messages when capturing with movie recorder. TG
<li><p>Change movie command "loop" keyword to "roundtrip". TG
</ul>

<p><b>April 6, 2007.  Version 1.2372.</b></p>

<ul type=None>
<li><p>Included C++ header files in Chimera distributions. TG
<li><p>Restricted movie recorder to PNG image format when raytracing. TG
</ul>

<p><b>April 5, 2007.  Version 1.2370.</b></p>

<ul type=None>

<li><p>Added movie recorder option to play frames forward then backward when encoding. Also added movie command "loop" option to permit this. TG
<li><p>Added raytracing option to movie recorder. TG
</ul>

<p><b>April 3, 2007.  Version 1.2369.</b></p>

<ul type=None>
<li><p>Added supersampling option to movie recorder. TG
</ul>

<p><b>March 28, 2007.  Version 1.2366.</b></p>

<ul type=None>
<li><p>Made volume viewer, scale bar, path tracer, and multiscale use model number offset when restoring a session an merging an already opened session.  TG
<li><p>Made scale bar, path tracer, and multiscale preserve model numbers when
session is restored. TG

</ul>

<p><b>March 27, 2007.  Version 1.2365.</b></p>

<ul type=None>
<li><p>Made measure volume/area tool automatically update as surface changes. TG
</ul>

<p><b>March 9, 2007.  Version 1.2354.</b></p>

<ul type=None>
<li><p>Made session restore of volume data sets use original model numbers. TG
</ul>

}}}